HEADER OXIDOREDUCTASE 08-AUG-05 2D0T TITLE CRYSTAL STRUCTURE OF 4-PHENYLIMIDAZOLE BOUND FORM OF HUMAN INDOLEAMINE TITLE 2 2,3-DIOXYGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INDOLEAMINE 2,3-DIOXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IDO, INDOLEAMINE-PYRROLE 2,3-DIOXYGENASE; COMPND 5 EC: 1.13.11.42; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODONPLUS-RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS HELIX BUNDLE, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 2 STRUCTURAL GENOMICS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.SUGIMOTO,S.ODA,T.OTSUKI,T.HINO,T.YOSHIDA,Y.SHIRO,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 30-OCT-24 2D0T 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2D0T 1 VERSN REVDAT 2 16-MAY-06 2D0T 1 JRNL REVDAT 1 31-JAN-06 2D0T 0 JRNL AUTH H.SUGIMOTO,S.ODA,T.OTSUKI,T.HINO,T.YOSHIDA,Y.SHIRO JRNL TITL CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE: JRNL TITL 2 CATALYTIC MECHANISM OF O2 INCORPORATION BY A HEME-CONTAINING JRNL TITL 3 DIOXYGENASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 2611 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16477023 JRNL DOI 10.1073/PNAS.0508996103 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2775764.420 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 45261 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2179 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5773 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 284 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5920 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 160 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -13.80000 REMARK 3 B22 (A**2) : 4.49000 REMARK 3 B33 (A**2) : 9.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.38 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.43 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.910 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 35.36 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2D0T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000024846. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9780, 1.7377, 1.7400, 1.7350, REMARK 200 1.7420, 1.7388 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48799 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.1 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : 0.05300 REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.28300 REMARK 200 R SYM FOR SHELL (I) : 0.28300 REMARK 200 FOR SHELL : 1.950 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, CHES, AMMONIUM ACETATE, PH REMARK 280 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 43.03500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.47550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.01350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.47550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.03500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.01350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL ASSEMGLY IS A MONOMER. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 HIS A 3 REMARK 465 ALA A 4 REMARK 465 MET A 5 REMARK 465 GLU A 6 REMARK 465 ASN A 7 REMARK 465 SER A 8 REMARK 465 TRP A 9 REMARK 465 THR A 10 REMARK 465 ILE A 11 REMARK 465 GLN A 361 REMARK 465 PRO A 362 REMARK 465 LYS A 363 REMARK 465 GLU A 364 REMARK 465 ASN A 365 REMARK 465 LYS A 366 REMARK 465 THR A 367 REMARK 465 SER A 368 REMARK 465 GLU A 369 REMARK 465 ASP A 370 REMARK 465 PRO A 371 REMARK 465 SER A 372 REMARK 465 LYS A 373 REMARK 465 LEU A 374 REMARK 465 GLU A 375 REMARK 465 ALA A 376 REMARK 465 LYS A 377 REMARK 465 GLY A 378 REMARK 465 THR A 379 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 HIS B 3 REMARK 465 ALA B 4 REMARK 465 MET B 5 REMARK 465 GLU B 6 REMARK 465 ASN B 7 REMARK 465 SER B 8 REMARK 465 TRP B 9 REMARK 465 THR B 10 REMARK 465 GLN B 361 REMARK 465 PRO B 362 REMARK 465 LYS B 363 REMARK 465 GLU B 364 REMARK 465 ASN B 365 REMARK 465 LYS B 366 REMARK 465 THR B 367 REMARK 465 SER B 368 REMARK 465 GLU B 369 REMARK 465 ASP B 370 REMARK 465 PRO B 371 REMARK 465 SER B 372 REMARK 465 LYS B 373 REMARK 465 LEU B 374 REMARK 465 GLU B 375 REMARK 465 ALA B 376 REMARK 465 LYS B 377 REMARK 465 GLY B 378 REMARK 465 THR B 379 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N LYS A 94 OXT GLY B 403 3655 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 308 CA - CB - SG ANGL. DEV. = 8.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 14 36.92 -61.21 REMARK 500 TYR A 15 14.28 -69.18 REMARK 500 ASN A 27 73.46 30.93 REMARK 500 VAL A 130 -62.42 -124.10 REMARK 500 ASN A 133 50.91 -96.18 REMARK 500 VAL A 229 -73.34 -118.41 REMARK 500 LEU A 243 45.26 -141.69 REMARK 500 SER A 244 -59.21 -22.39 REMARK 500 ILE A 354 -56.51 -129.97 REMARK 500 LYS B 13 -143.44 -88.26 REMARK 500 ASN B 27 75.35 33.05 REMARK 500 ASP B 128 -64.44 -91.43 REMARK 500 ASN B 133 51.45 -100.78 REMARK 500 VAL B 229 -77.08 -119.15 REMARK 500 LEU B 243 46.15 -143.10 REMARK 500 SER B 244 -64.43 -21.77 REMARK 500 GLU B 254 -72.68 -57.62 REMARK 500 ILE B 354 -52.62 -135.18 REMARK 500 GLU B 402 96.99 75.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 404 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 346 NE2 REMARK 620 2 HEM A 404 NA 91.7 REMARK 620 3 HEM A 404 NB 92.8 92.8 REMARK 620 4 HEM A 404 NC 91.0 177.3 87.2 REMARK 620 5 HEM A 404 ND 89.0 90.3 176.4 89.6 REMARK 620 6 PIM A 501 N3 179.0 87.4 87.5 89.9 90.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 404 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 346 NE2 REMARK 620 2 HEM B 404 NA 88.0 REMARK 620 3 HEM B 404 NB 94.7 94.5 REMARK 620 4 HEM B 404 NC 94.2 177.8 85.8 REMARK 620 5 HEM B 404 ND 87.1 87.1 177.6 92.6 REMARK 620 6 PIM B1501 N3 177.1 90.4 87.7 87.5 90.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PIM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHE A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHE A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PIM B 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHE B 1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHE B 1503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D0U RELATED DB: PDB REMARK 900 LIGAND WAS EXCHANGED FROM PHENYLIMIDAZOLE TO CYANIDE REMARK 900 RELATED ID: MY_001000021.1 RELATED DB: TARGETDB DBREF 2D0T A 1 403 UNP P14902 I23O_HUMAN 1 403 DBREF 2D0T B 1 403 UNP P14902 I23O_HUMAN 1 403 SEQADV 2D0T GLY A -2 UNP P14902 CLONING ARTIFACT SEQADV 2D0T SER A -1 UNP P14902 CLONING ARTIFACT SEQADV 2D0T HIS A 0 UNP P14902 CLONING ARTIFACT SEQADV 2D0T GLY B -2 UNP P14902 CLONING ARTIFACT SEQADV 2D0T SER B -1 UNP P14902 CLONING ARTIFACT SEQADV 2D0T HIS B 0 UNP P14902 CLONING ARTIFACT SEQRES 1 A 406 GLY SER HIS MET ALA HIS ALA MET GLU ASN SER TRP THR SEQRES 2 A 406 ILE SER LYS GLU TYR HIS ILE ASP GLU GLU VAL GLY PHE SEQRES 3 A 406 ALA LEU PRO ASN PRO GLN GLU ASN LEU PRO ASP PHE TYR SEQRES 4 A 406 ASN ASP TRP MET PHE ILE ALA LYS HIS LEU PRO ASP LEU SEQRES 5 A 406 ILE GLU SER GLY GLN LEU ARG GLU ARG VAL GLU LYS LEU SEQRES 6 A 406 ASN MET LEU SER ILE ASP HIS LEU THR ASP HIS LYS SER SEQRES 7 A 406 GLN ARG LEU ALA ARG LEU VAL LEU GLY CYS ILE THR MET SEQRES 8 A 406 ALA TYR VAL TRP GLY LYS GLY HIS GLY ASP VAL ARG LYS SEQRES 9 A 406 VAL LEU PRO ARG ASN ILE ALA VAL PRO TYR CYS GLN LEU SEQRES 10 A 406 SER LYS LYS LEU GLU LEU PRO PRO ILE LEU VAL TYR ALA SEQRES 11 A 406 ASP CYS VAL LEU ALA ASN TRP LYS LYS LYS ASP PRO ASN SEQRES 12 A 406 LYS PRO LEU THR TYR GLU ASN MET ASP VAL LEU PHE SER SEQRES 13 A 406 PHE ARG ASP GLY ASP CYS SER LYS GLY PHE PHE LEU VAL SEQRES 14 A 406 SER LEU LEU VAL GLU ILE ALA ALA ALA SER ALA ILE LYS SEQRES 15 A 406 VAL ILE PRO THR VAL PHE LYS ALA MET GLN MET GLN GLU SEQRES 16 A 406 ARG ASP THR LEU LEU LYS ALA LEU LEU GLU ILE ALA SER SEQRES 17 A 406 CYS LEU GLU LYS ALA LEU GLN VAL PHE HIS GLN ILE HIS SEQRES 18 A 406 ASP HIS VAL ASN PRO LYS ALA PHE PHE SER VAL LEU ARG SEQRES 19 A 406 ILE TYR LEU SER GLY TRP LYS GLY ASN PRO GLN LEU SER SEQRES 20 A 406 ASP GLY LEU VAL TYR GLU GLY PHE TRP GLU ASP PRO LYS SEQRES 21 A 406 GLU PHE ALA GLY GLY SER ALA GLY GLN SER SER VAL PHE SEQRES 22 A 406 GLN CYS PHE ASP VAL LEU LEU GLY ILE GLN GLN THR ALA SEQRES 23 A 406 GLY GLY GLY HIS ALA ALA GLN PHE LEU GLN ASP MET ARG SEQRES 24 A 406 ARG TYR MET PRO PRO ALA HIS ARG ASN PHE LEU CYS SER SEQRES 25 A 406 LEU GLU SER ASN PRO SER VAL ARG GLU PHE VAL LEU SER SEQRES 26 A 406 LYS GLY ASP ALA GLY LEU ARG GLU ALA TYR ASP ALA CYS SEQRES 27 A 406 VAL LYS ALA LEU VAL SER LEU ARG SER TYR HIS LEU GLN SEQRES 28 A 406 ILE VAL THR LYS TYR ILE LEU ILE PRO ALA SER GLN GLN SEQRES 29 A 406 PRO LYS GLU ASN LYS THR SER GLU ASP PRO SER LYS LEU SEQRES 30 A 406 GLU ALA LYS GLY THR GLY GLY THR ASP LEU MET ASN PHE SEQRES 31 A 406 LEU LYS THR VAL ARG SER THR THR GLU LYS SER LEU LEU SEQRES 32 A 406 LYS GLU GLY SEQRES 1 B 406 GLY SER HIS MET ALA HIS ALA MET GLU ASN SER TRP THR SEQRES 2 B 406 ILE SER LYS GLU TYR HIS ILE ASP GLU GLU VAL GLY PHE SEQRES 3 B 406 ALA LEU PRO ASN PRO GLN GLU ASN LEU PRO ASP PHE TYR SEQRES 4 B 406 ASN ASP TRP MET PHE ILE ALA LYS HIS LEU PRO ASP LEU SEQRES 5 B 406 ILE GLU SER GLY GLN LEU ARG GLU ARG VAL GLU LYS LEU SEQRES 6 B 406 ASN MET LEU SER ILE ASP HIS LEU THR ASP HIS LYS SER SEQRES 7 B 406 GLN ARG LEU ALA ARG LEU VAL LEU GLY CYS ILE THR MET SEQRES 8 B 406 ALA TYR VAL TRP GLY LYS GLY HIS GLY ASP VAL ARG LYS SEQRES 9 B 406 VAL LEU PRO ARG ASN ILE ALA VAL PRO TYR CYS GLN LEU SEQRES 10 B 406 SER LYS LYS LEU GLU LEU PRO PRO ILE LEU VAL TYR ALA SEQRES 11 B 406 ASP CYS VAL LEU ALA ASN TRP LYS LYS LYS ASP PRO ASN SEQRES 12 B 406 LYS PRO LEU THR TYR GLU ASN MET ASP VAL LEU PHE SER SEQRES 13 B 406 PHE ARG ASP GLY ASP CYS SER LYS GLY PHE PHE LEU VAL SEQRES 14 B 406 SER LEU LEU VAL GLU ILE ALA ALA ALA SER ALA ILE LYS SEQRES 15 B 406 VAL ILE PRO THR VAL PHE LYS ALA MET GLN MET GLN GLU SEQRES 16 B 406 ARG ASP THR LEU LEU LYS ALA LEU LEU GLU ILE ALA SER SEQRES 17 B 406 CYS LEU GLU LYS ALA LEU GLN VAL PHE HIS GLN ILE HIS SEQRES 18 B 406 ASP HIS VAL ASN PRO LYS ALA PHE PHE SER VAL LEU ARG SEQRES 19 B 406 ILE TYR LEU SER GLY TRP LYS GLY ASN PRO GLN LEU SER SEQRES 20 B 406 ASP GLY LEU VAL TYR GLU GLY PHE TRP GLU ASP PRO LYS SEQRES 21 B 406 GLU PHE ALA GLY GLY SER ALA GLY GLN SER SER VAL PHE SEQRES 22 B 406 GLN CYS PHE ASP VAL LEU LEU GLY ILE GLN GLN THR ALA SEQRES 23 B 406 GLY GLY GLY HIS ALA ALA GLN PHE LEU GLN ASP MET ARG SEQRES 24 B 406 ARG TYR MET PRO PRO ALA HIS ARG ASN PHE LEU CYS SER SEQRES 25 B 406 LEU GLU SER ASN PRO SER VAL ARG GLU PHE VAL LEU SER SEQRES 26 B 406 LYS GLY ASP ALA GLY LEU ARG GLU ALA TYR ASP ALA CYS SEQRES 27 B 406 VAL LYS ALA LEU VAL SER LEU ARG SER TYR HIS LEU GLN SEQRES 28 B 406 ILE VAL THR LYS TYR ILE LEU ILE PRO ALA SER GLN GLN SEQRES 29 B 406 PRO LYS GLU ASN LYS THR SER GLU ASP PRO SER LYS LEU SEQRES 30 B 406 GLU ALA LYS GLY THR GLY GLY THR ASP LEU MET ASN PHE SEQRES 31 B 406 LEU LYS THR VAL ARG SER THR THR GLU LYS SER LEU LEU SEQRES 32 B 406 LYS GLU GLY HET HEM A 404 43 HET PIM A 501 11 HET NHE A 502 13 HET NHE A 503 13 HET HEM B 404 43 HET PIM B1501 11 HET NHE B1502 13 HET NHE B1503 13 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM PIM 4-PHENYL-1H-IMIDAZOLE HETNAM NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID HETSYN HEM HEME HETSYN NHE N-CYCLOHEXYLTAURINE; CHES FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 PIM 2(C9 H8 N2) FORMUL 5 NHE 4(C8 H17 N O3 S) FORMUL 11 HOH *138(H2 O) HELIX 1 1 PRO A 33 PHE A 35 5 3 HELIX 2 2 TYR A 36 HIS A 45 1 10 HELIX 3 3 HIS A 45 SER A 52 1 8 HELIX 4 4 GLN A 54 LEU A 62 1 9 HELIX 5 5 ASP A 72 GLY A 93 1 22 HELIX 6 6 PRO A 104 GLU A 119 1 16 HELIX 7 7 VAL A 125 VAL A 130 1 6 HELIX 8 8 THR A 144 GLU A 146 5 3 HELIX 9 9 CYS A 159 LYS A 179 1 21 HELIX 10 10 VAL A 180 MET A 190 1 11 HELIX 11 11 GLU A 192 HIS A 215 1 24 HELIX 12 12 GLN A 216 VAL A 221 1 6 HELIX 13 13 ASN A 222 VAL A 229 1 8 HELIX 14 14 VAL A 229 LEU A 234 1 6 HELIX 15 15 ASN A 240 SER A 244 5 5 HELIX 16 16 SER A 263 GLN A 266 5 4 HELIX 17 17 SER A 267 LEU A 277 1 11 HELIX 18 18 GLY A 286 ARG A 296 1 11 HELIX 19 19 ARG A 297 MET A 299 5 3 HELIX 20 20 PRO A 300 SER A 312 1 13 HELIX 21 21 SER A 315 SER A 322 1 8 HELIX 22 22 ASP A 325 ILE A 354 1 30 HELIX 23 23 ILE A 354 SER A 359 1 6 HELIX 24 24 GLY A 381 SER A 398 1 18 HELIX 25 25 PRO B 33 PHE B 35 5 3 HELIX 26 26 TYR B 36 HIS B 45 1 10 HELIX 27 27 HIS B 45 SER B 52 1 8 HELIX 28 28 GLN B 54 LYS B 61 1 8 HELIX 29 29 ASP B 72 GLY B 93 1 22 HELIX 30 30 PRO B 104 GLU B 119 1 16 HELIX 31 31 VAL B 125 VAL B 130 1 6 HELIX 32 32 THR B 144 GLU B 146 5 3 HELIX 33 33 CYS B 159 LYS B 179 1 21 HELIX 34 34 VAL B 180 GLN B 191 1 12 HELIX 35 35 GLU B 192 HIS B 215 1 24 HELIX 36 36 GLN B 216 VAL B 221 1 6 HELIX 37 37 ASN B 222 VAL B 229 1 8 HELIX 38 38 VAL B 229 LEU B 234 1 6 HELIX 39 39 ASN B 240 SER B 244 5 5 HELIX 40 40 SER B 263 GLN B 266 5 4 HELIX 41 41 SER B 267 LEU B 277 1 11 HELIX 42 42 GLY B 286 ARG B 296 1 11 HELIX 43 43 ARG B 297 MET B 299 5 3 HELIX 44 44 PRO B 300 SER B 312 1 13 HELIX 45 45 SER B 315 LYS B 323 1 9 HELIX 46 46 ASP B 325 ILE B 354 1 30 HELIX 47 47 ILE B 354 SER B 359 1 6 HELIX 48 48 GLY B 381 SER B 398 1 18 SHEET 1 A 2 VAL A 102 LEU A 103 0 SHEET 2 A 2 VAL A 248 TYR A 249 1 O VAL A 248 N LEU A 103 SHEET 1 B 2 TRP A 134 LYS A 136 0 SHEET 2 B 2 MET A 148 VAL A 150 -1 O ASP A 149 N LYS A 135 SHEET 1 C 2 VAL B 102 LEU B 103 0 SHEET 2 C 2 VAL B 248 TYR B 249 1 O VAL B 248 N LEU B 103 SHEET 1 D 2 LYS B 135 LYS B 136 0 SHEET 2 D 2 MET B 148 ASP B 149 -1 O ASP B 149 N LYS B 135 SSBOND 1 CYS A 308 CYS B 308 1555 1555 2.05 LINK NE2 HIS A 346 FE HEM A 404 1555 1555 2.09 LINK FE HEM A 404 N3 PIM A 501 1555 1555 2.13 LINK NE2 HIS B 346 FE HEM B 404 1555 1555 2.11 LINK FE HEM B 404 N3 PIM B1501 1555 1555 2.13 SITE 1 AC1 17 PHE A 163 SER A 167 PHE A 214 PHE A 226 SITE 2 AC1 17 SER A 263 ALA A 264 ARG A 343 HIS A 346 SITE 3 AC1 17 ILE A 349 VAL A 350 LEU A 384 VAL A 391 SITE 4 AC1 17 PIM A 501 NHE A 502 NHE A 503 HOH A 506 SITE 5 AC1 17 HOH A 514 SITE 1 AC2 18 PHE B 163 SER B 167 PHE B 214 ILE B 217 SITE 2 AC2 18 PHE B 226 SER B 263 ALA B 264 ARG B 343 SITE 3 AC2 18 HIS B 346 ILE B 349 VAL B 350 ILE B 354 SITE 4 AC2 18 LEU B 384 VAL B 391 PIM B1501 NHE B1502 SITE 5 AC2 18 NHE B1503 HOH B1509 SITE 1 AC3 8 VAL A 130 PHE A 163 PHE A 164 SER A 167 SITE 2 AC3 8 SER A 263 ALA A 264 HEM A 404 NHE A 502 SITE 1 AC4 8 LEU A 234 GLY A 236 ALA A 260 GLY A 261 SITE 2 AC4 8 GLY A 262 HEM A 404 PIM A 501 NHE A 503 SITE 1 AC5 3 LEU A 384 HEM A 404 NHE A 502 SITE 1 AC6 7 VAL B 130 PHE B 163 SER B 167 SER B 263 SITE 2 AC6 7 ALA B 264 HEM B 404 NHE B1502 SITE 1 AC7 7 LEU B 234 GLY B 236 ALA B 260 GLY B 261 SITE 2 AC7 7 GLY B 262 HEM B 404 PIM B1501 SITE 1 AC8 3 HIS B 287 LEU B 384 HEM B 404 CRYST1 86.070 98.027 130.951 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011618 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010201 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007636 0.00000 CONECT 2370 5335 CONECT 2662 5965 CONECT 5335 2370 CONECT 5627 6045 CONECT 5923 5927 5954 CONECT 5924 5930 5937 CONECT 5925 5940 5944 CONECT 5926 5947 5951 CONECT 5927 5923 5928 5961 CONECT 5928 5927 5929 5932 CONECT 5929 5928 5930 5931 CONECT 5930 5924 5929 5961 CONECT 5931 5929 CONECT 5932 5928 5933 CONECT 5933 5932 5934 CONECT 5934 5933 5935 5936 CONECT 5935 5934 CONECT 5936 5934 CONECT 5937 5924 5938 5962 CONECT 5938 5937 5939 5941 CONECT 5939 5938 5940 5942 CONECT 5940 5925 5939 5962 CONECT 5941 5938 CONECT 5942 5939 5943 CONECT 5943 5942 CONECT 5944 5925 5945 5963 CONECT 5945 5944 5946 5948 CONECT 5946 5945 5947 5949 CONECT 5947 5926 5946 5963 CONECT 5948 5945 CONECT 5949 5946 5950 CONECT 5950 5949 CONECT 5951 5926 5952 5964 CONECT 5952 5951 5953 5955 CONECT 5953 5952 5954 5956 CONECT 5954 5923 5953 5964 CONECT 5955 5952 CONECT 5956 5953 5957 CONECT 5957 5956 5958 CONECT 5958 5957 5959 5960 CONECT 5959 5958 CONECT 5960 5958 CONECT 5961 5927 5930 5965 CONECT 5962 5937 5940 5965 CONECT 5963 5944 5947 5965 CONECT 5964 5951 5954 5965 CONECT 5965 2662 5961 5962 5963 CONECT 5965 5964 5968 CONECT 5966 5967 5970 CONECT 5967 5966 5968 CONECT 5968 5965 5967 5969 CONECT 5969 5968 5970 CONECT 5970 5966 5969 5971 CONECT 5971 5970 5972 5976 CONECT 5972 5971 5973 CONECT 5973 5972 5974 CONECT 5974 5973 5975 CONECT 5975 5974 5976 CONECT 5976 5971 5975 CONECT 5977 5978 5989 CONECT 5978 5977 5979 CONECT 5979 5978 5980 5981 CONECT 5980 5979 5988 CONECT 5981 5979 5982 CONECT 5982 5981 5983 CONECT 5983 5982 5984 CONECT 5984 5983 5985 5986 5987 CONECT 5985 5984 CONECT 5986 5984 CONECT 5987 5984 CONECT 5988 5980 5989 CONECT 5989 5977 5988 CONECT 5990 5991 6002 CONECT 5991 5990 5992 CONECT 5992 5991 5993 5994 CONECT 5993 5992 6001 CONECT 5994 5992 5995 CONECT 5995 5994 5996 CONECT 5996 5995 5997 CONECT 5997 5996 5998 5999 6000 CONECT 5998 5997 CONECT 5999 5997 CONECT 6000 5997 CONECT 6001 5993 6002 CONECT 6002 5990 6001 CONECT 6003 6007 6034 CONECT 6004 6010 6017 CONECT 6005 6020 6024 CONECT 6006 6027 6031 CONECT 6007 6003 6008 6041 CONECT 6008 6007 6009 6012 CONECT 6009 6008 6010 6011 CONECT 6010 6004 6009 6041 CONECT 6011 6009 CONECT 6012 6008 6013 CONECT 6013 6012 6014 CONECT 6014 6013 6015 6016 CONECT 6015 6014 CONECT 6016 6014 CONECT 6017 6004 6018 6042 CONECT 6018 6017 6019 6021 CONECT 6019 6018 6020 6022 CONECT 6020 6005 6019 6042 CONECT 6021 6018 CONECT 6022 6019 6023 CONECT 6023 6022 CONECT 6024 6005 6025 6043 CONECT 6025 6024 6026 6028 CONECT 6026 6025 6027 6029 CONECT 6027 6006 6026 6043 CONECT 6028 6025 CONECT 6029 6026 6030 CONECT 6030 6029 CONECT 6031 6006 6032 6044 CONECT 6032 6031 6033 6035 CONECT 6033 6032 6034 6036 CONECT 6034 6003 6033 6044 CONECT 6035 6032 CONECT 6036 6033 6037 CONECT 6037 6036 6038 CONECT 6038 6037 6039 6040 CONECT 6039 6038 CONECT 6040 6038 CONECT 6041 6007 6010 6045 CONECT 6042 6017 6020 6045 CONECT 6043 6024 6027 6045 CONECT 6044 6031 6034 6045 CONECT 6045 5627 6041 6042 6043 CONECT 6045 6044 6048 CONECT 6046 6047 6050 CONECT 6047 6046 6048 CONECT 6048 6045 6047 6049 CONECT 6049 6048 6050 CONECT 6050 6046 6049 6051 CONECT 6051 6050 6052 6056 CONECT 6052 6051 6053 CONECT 6053 6052 6054 CONECT 6054 6053 6055 CONECT 6055 6054 6056 CONECT 6056 6051 6055 CONECT 6057 6058 6069 CONECT 6058 6057 6059 CONECT 6059 6058 6060 6061 CONECT 6060 6059 6068 CONECT 6061 6059 6062 CONECT 6062 6061 6063 CONECT 6063 6062 6064 CONECT 6064 6063 6065 6066 6067 CONECT 6065 6064 CONECT 6066 6064 CONECT 6067 6064 CONECT 6068 6060 6069 CONECT 6069 6057 6068 CONECT 6070 6071 6082 CONECT 6071 6070 6072 CONECT 6072 6071 6073 6074 CONECT 6073 6072 6081 CONECT 6074 6072 6075 CONECT 6075 6074 6076 CONECT 6076 6075 6077 CONECT 6077 6076 6078 6079 6080 CONECT 6078 6077 CONECT 6079 6077 CONECT 6080 6077 CONECT 6081 6073 6082 CONECT 6082 6070 6081 MASTER 427 0 8 48 8 0 20 6 6218 2 166 64 END