HEADER TRANSFERASE 25-OCT-16 5M6R TITLE HUMAN PORPHOBILINOGEN DEAMINASE IN COMPLEX WITH REACTION INTERMEDIATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORPHOBILINOGEN DEAMINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PBG-D,HYDROXYMETHYLBILANE SYNTHASE,HMBS,PRE-UROPORPHYRINOGEN COMPND 5 SYNTHASE; COMPND 6 EC: 2.5.1.61; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HMBS, PBGD, UPS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PORPHOBILINOGEN DEAMINASE, HEME BIOSYNTHESIS, PORPHYRIA, HMBS, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.PLUTA,O.MILLET,P.ROVERSI,A.L.ROJAS,S.GU REVDAT 4 17-JAN-24 5M6R 1 REMARK REVDAT 3 29-MAY-19 5M6R 1 JRNL REVDAT 2 31-JAN-18 5M6R 1 REMARK REVDAT 1 15-NOV-17 5M6R 0 JRNL AUTH P.PLUTA,P.ROVERSI,G.BERNARDO-SEISDEDOS,A.L.ROJAS,J.B.COOPER, JRNL AUTH 2 S.GU,R.W.PICKERSGILL,O.MILLET JRNL TITL STRUCTURAL BASIS OF PYRROLE POLYMERIZATION IN HUMAN JRNL TITL 2 PORPHOBILINOGEN DEAMINASE. JRNL REF BIOCHIM BIOPHYS ACTA GEN V.1862 1948 2018 JRNL REF 2 SUBJ JRNL REFN ISSN 0304-4165 JRNL PMID 29908816 JRNL DOI 10.1016/J.BBAGEN.2018.06.013 REMARK 2 REMARK 2 RESOLUTION. 2.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 22510 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 + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1104 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 11 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.73 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.95 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2433 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2410 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2306 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.22 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 127 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5099 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 150 REMARK 3 SOLVENT ATOMS : 23 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -13.37360 REMARK 3 B22 (A**2) : 32.36340 REMARK 3 B33 (A**2) : -18.98980 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -47.06890 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.460 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.822 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.317 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.883 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.858 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 10665 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 19364 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2414 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 132 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 1663 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 10665 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 687 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 11840 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.14 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.18 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.70 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -15.2439 0.8914 2.1699 REMARK 3 T TENSOR REMARK 3 T11: -0.1366 T22: -0.3854 REMARK 3 T33: -0.0125 T12: -0.0400 REMARK 3 T13: 0.2440 T23: -0.0635 REMARK 3 L TENSOR REMARK 3 L11: 2.1377 L22: 3.4544 REMARK 3 L33: 1.9639 L12: -0.5325 REMARK 3 L13: -1.4042 L23: 0.0190 REMARK 3 S TENSOR REMARK 3 S11: -0.2162 S12: 0.2960 S13: -0.3389 REMARK 3 S21: -0.0234 S22: 0.0105 S23: 0.4829 REMARK 3 S31: 0.1171 S32: -0.4124 S33: 0.2057 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): -32.9844 26.0720 25.7030 REMARK 3 T TENSOR REMARK 3 T11: -0.1177 T22: -0.4977 REMARK 3 T33: 0.0423 T12: 0.0523 REMARK 3 T13: 0.3332 T23: 0.0424 REMARK 3 L TENSOR REMARK 3 L11: 2.1768 L22: 3.1626 REMARK 3 L33: 3.5809 L12: 0.0767 REMARK 3 L13: -2.2414 L23: 0.2005 REMARK 3 S TENSOR REMARK 3 S11: 0.2093 S12: 0.2053 S13: 0.1627 REMARK 3 S21: 0.2536 S22: 0.0322 S23: 0.4156 REMARK 3 S31: -0.2817 S32: -0.2356 S33: -0.2415 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5M6R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200002012. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972422 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION MAY 1, 2016 REMARK 200 DATA SCALING SOFTWARE : AIMLESS VERSION 0.5.23 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22971 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.730 REMARK 200 RESOLUTION RANGE LOW (A) : 81.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.19400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 1.37700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3ECR REMARK 200 REMARK 200 REMARK: PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA HEPES PH 7.2, 0.9 M NA REMARK 280 DIHYDROGEN PHOSPHATE/0.9 M K DIHYDROGEN PHOSPHATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 40.60000 REMARK 290 SMTRY3 2 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 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 MET A -27 REMARK 465 LYS A -26 REMARK 465 HIS A -25 REMARK 465 HIS A -24 REMARK 465 HIS A -23 REMARK 465 HIS A -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 PRO A -19 REMARK 465 MET A -18 REMARK 465 SER A -17 REMARK 465 ASP A -16 REMARK 465 TYR A -15 REMARK 465 ASP A -14 REMARK 465 ILE A -13 REMARK 465 PRO A -12 REMARK 465 THR A -11 REMARK 465 THR A -10 REMARK 465 GLU A -9 REMARK 465 ASN A -8 REMARK 465 LEU A -7 REMARK 465 TYR A -6 REMARK 465 PHE A -5 REMARK 465 GLN A -4 REMARK 465 GLY A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 GLY A 3 REMARK 465 ASN A 4 REMARK 465 GLY A 5 REMARK 465 ASN A 6 REMARK 465 ALA A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 THR A 10 REMARK 465 ALA A 11 REMARK 465 GLU A 12 REMARK 465 GLU A 13 REMARK 465 ASN A 14 REMARK 465 SER A 15 REMARK 465 PRO A 16 REMARK 465 LYS A 17 REMARK 465 ASN A 358 REMARK 465 ASP A 359 REMARK 465 ALA A 360 REMARK 465 HIS A 361 REMARK 465 MET B -27 REMARK 465 LYS B -26 REMARK 465 HIS B -25 REMARK 465 HIS B -24 REMARK 465 HIS B -23 REMARK 465 HIS B -22 REMARK 465 HIS B -21 REMARK 465 HIS B -20 REMARK 465 PRO B -19 REMARK 465 MET B -18 REMARK 465 SER B -17 REMARK 465 ASP B -16 REMARK 465 TYR B -15 REMARK 465 ASP B -14 REMARK 465 ILE B -13 REMARK 465 PRO B -12 REMARK 465 THR B -11 REMARK 465 THR B -10 REMARK 465 GLU B -9 REMARK 465 ASN B -8 REMARK 465 LEU B -7 REMARK 465 TYR B -6 REMARK 465 PHE B -5 REMARK 465 GLN B -4 REMARK 465 GLY B -3 REMARK 465 ALA B -2 REMARK 465 MET B -1 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 GLY B 3 REMARK 465 ASN B 4 REMARK 465 GLY B 5 REMARK 465 ASN B 6 REMARK 465 ALA B 7 REMARK 465 ALA B 8 REMARK 465 ALA B 9 REMARK 465 THR B 10 REMARK 465 ALA B 11 REMARK 465 GLU B 12 REMARK 465 GLU B 13 REMARK 465 ASN B 14 REMARK 465 SER B 15 REMARK 465 PRO B 16 REMARK 465 LYS B 17 REMARK 465 LYS B 62 REMARK 465 ILE B 63 REMARK 465 LEU B 64 REMARK 465 ASP B 65 REMARK 465 THR B 66 REMARK 465 ALA B 67 REMARK 465 LEU B 68 REMARK 465 SER B 69 REMARK 465 LYS B 70 REMARK 465 ILE B 71 REMARK 465 GLY B 72 REMARK 465 GLU B 73 REMARK 465 LYS B 74 REMARK 465 SER B 75 REMARK 465 ALA B 354 REMARK 465 ARG B 355 REMARK 465 GLN B 356 REMARK 465 LEU B 357 REMARK 465 ASN B 358 REMARK 465 ASP B 359 REMARK 465 ALA B 360 REMARK 465 HIS B 361 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 LYS A 27 2.42 -69.30 REMARK 500 LEU A 68 4.53 -69.86 REMARK 500 LYS A 70 87.25 -151.66 REMARK 500 SER A 75 44.35 -97.83 REMARK 500 PRO A 127 -19.54 -46.54 REMARK 500 PHE A 129 49.82 -87.34 REMARK 500 PHE A 158 78.72 -109.30 REMARK 500 CYS A 261 -67.73 -164.35 REMARK 500 ASP A 307 74.95 -103.14 REMARK 500 ALA A 320 57.44 -143.35 REMARK 500 ARG B 19 90.18 -61.51 REMARK 500 LYS B 27 74.71 -68.84 REMARK 500 PRO B 127 -17.50 -48.24 REMARK 500 PHE B 158 78.40 -109.11 REMARK 500 CYS B 261 -69.22 -163.88 REMARK 500 ASP B 307 75.01 -103.78 REMARK 500 ALA B 320 56.87 -143.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7J8 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide 7J8 B 401 and CYS B REMARK 800 261 DBREF 5M6R A 1 361 UNP P08397 HEM3_HUMAN 1 361 DBREF 5M6R B 1 361 UNP P08397 HEM3_HUMAN 1 361 SEQADV 5M6R MET A -27 UNP P08397 INITIATING METHIONINE SEQADV 5M6R LYS A -26 UNP P08397 EXPRESSION TAG SEQADV 5M6R HIS A -25 UNP P08397 EXPRESSION TAG SEQADV 5M6R HIS A -24 UNP P08397 EXPRESSION TAG SEQADV 5M6R HIS A -23 UNP P08397 EXPRESSION TAG SEQADV 5M6R HIS A -22 UNP P08397 EXPRESSION TAG SEQADV 5M6R HIS A -21 UNP P08397 EXPRESSION TAG SEQADV 5M6R HIS A -20 UNP P08397 EXPRESSION TAG SEQADV 5M6R PRO A -19 UNP P08397 EXPRESSION TAG SEQADV 5M6R MET A -18 UNP P08397 EXPRESSION TAG SEQADV 5M6R SER A -17 UNP P08397 EXPRESSION TAG SEQADV 5M6R ASP A -16 UNP P08397 EXPRESSION TAG SEQADV 5M6R TYR A -15 UNP P08397 EXPRESSION TAG SEQADV 5M6R ASP A -14 UNP P08397 EXPRESSION TAG SEQADV 5M6R ILE A -13 UNP P08397 EXPRESSION TAG SEQADV 5M6R PRO A -12 UNP P08397 EXPRESSION TAG SEQADV 5M6R THR A -11 UNP P08397 EXPRESSION TAG SEQADV 5M6R THR A -10 UNP P08397 EXPRESSION TAG SEQADV 5M6R GLU A -9 UNP P08397 EXPRESSION TAG SEQADV 5M6R ASN A -8 UNP P08397 EXPRESSION TAG SEQADV 5M6R LEU A -7 UNP P08397 EXPRESSION TAG SEQADV 5M6R TYR A -6 UNP P08397 EXPRESSION TAG SEQADV 5M6R PHE A -5 UNP P08397 EXPRESSION TAG SEQADV 5M6R GLN A -4 UNP P08397 EXPRESSION TAG SEQADV 5M6R GLY A -3 UNP P08397 EXPRESSION TAG SEQADV 5M6R ALA A -2 UNP P08397 EXPRESSION TAG SEQADV 5M6R MET A -1 UNP P08397 EXPRESSION TAG SEQADV 5M6R ALA A 0 UNP P08397 EXPRESSION TAG SEQADV 5M6R MET B -27 UNP P08397 INITIATING METHIONINE SEQADV 5M6R LYS B -26 UNP P08397 EXPRESSION TAG SEQADV 5M6R HIS B -25 UNP P08397 EXPRESSION TAG SEQADV 5M6R HIS B -24 UNP P08397 EXPRESSION TAG SEQADV 5M6R HIS B -23 UNP P08397 EXPRESSION TAG SEQADV 5M6R HIS B -22 UNP P08397 EXPRESSION TAG SEQADV 5M6R HIS B -21 UNP P08397 EXPRESSION TAG SEQADV 5M6R HIS B -20 UNP P08397 EXPRESSION TAG SEQADV 5M6R PRO B -19 UNP P08397 EXPRESSION TAG SEQADV 5M6R MET B -18 UNP P08397 EXPRESSION TAG SEQADV 5M6R SER B -17 UNP P08397 EXPRESSION TAG SEQADV 5M6R ASP B -16 UNP P08397 EXPRESSION TAG SEQADV 5M6R TYR B -15 UNP P08397 EXPRESSION TAG SEQADV 5M6R ASP B -14 UNP P08397 EXPRESSION TAG SEQADV 5M6R ILE B -13 UNP P08397 EXPRESSION TAG SEQADV 5M6R PRO B -12 UNP P08397 EXPRESSION TAG SEQADV 5M6R THR B -11 UNP P08397 EXPRESSION TAG SEQADV 5M6R THR B -10 UNP P08397 EXPRESSION TAG SEQADV 5M6R GLU B -9 UNP P08397 EXPRESSION TAG SEQADV 5M6R ASN B -8 UNP P08397 EXPRESSION TAG SEQADV 5M6R LEU B -7 UNP P08397 EXPRESSION TAG SEQADV 5M6R TYR B -6 UNP P08397 EXPRESSION TAG SEQADV 5M6R PHE B -5 UNP P08397 EXPRESSION TAG SEQADV 5M6R GLN B -4 UNP P08397 EXPRESSION TAG SEQADV 5M6R GLY B -3 UNP P08397 EXPRESSION TAG SEQADV 5M6R ALA B -2 UNP P08397 EXPRESSION TAG SEQADV 5M6R MET B -1 UNP P08397 EXPRESSION TAG SEQADV 5M6R ALA B 0 UNP P08397 EXPRESSION TAG SEQRES 1 A 389 MET LYS HIS HIS HIS HIS HIS HIS PRO MET SER ASP TYR SEQRES 2 A 389 ASP ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY ALA SEQRES 3 A 389 MET ALA MET SER GLY ASN GLY ASN ALA ALA ALA THR ALA SEQRES 4 A 389 GLU GLU ASN SER PRO LYS MET ARG VAL ILE ARG VAL GLY SEQRES 5 A 389 THR ARG LYS SER GLN LEU ALA ARG ILE GLN THR ASP SER SEQRES 6 A 389 VAL VAL ALA THR LEU LYS ALA SER TYR PRO GLY LEU GLN SEQRES 7 A 389 PHE GLU ILE ILE ALA MET SER THR THR GLY ASP LYS ILE SEQRES 8 A 389 LEU ASP THR ALA LEU SER LYS ILE GLY GLU LYS SER LEU SEQRES 9 A 389 PHE THR LYS GLU LEU GLU HIS ALA LEU GLU LYS ASN GLU SEQRES 10 A 389 VAL ASP LEU VAL VAL HIS SER LEU LYS ASP LEU PRO THR SEQRES 11 A 389 VAL LEU PRO PRO GLY PHE THR ILE GLY ALA ILE CYS LYS SEQRES 12 A 389 ARG GLU ASN PRO HIS ASP ALA VAL VAL PHE HIS PRO LYS SEQRES 13 A 389 PHE VAL GLY LYS THR LEU GLU THR LEU PRO GLU LYS SER SEQRES 14 A 389 VAL VAL GLY THR SER SER LEU ARG ARG ALA ALA GLN LEU SEQRES 15 A 389 GLN ARG LYS PHE PRO HIS LEU GLU PHE ARG SER ILE ARG SEQRES 16 A 389 GLY ASN LEU ASN THR ARG LEU ARG LYS LEU ASP GLU GLN SEQRES 17 A 389 GLN GLU PHE SER ALA ILE ILE LEU ALA THR ALA GLY LEU SEQRES 18 A 389 GLN ARG MET GLY TRP HIS ASN ARG VAL GLY GLN ILE LEU SEQRES 19 A 389 HIS PRO GLU GLU CYS MET TYR ALA VAL GLY GLN GLY ALA SEQRES 20 A 389 LEU GLY VAL GLU VAL ARG ALA LYS ASP GLN ASP ILE LEU SEQRES 21 A 389 ASP LEU VAL GLY VAL LEU HIS ASP PRO GLU THR LEU LEU SEQRES 22 A 389 ARG CYS ILE ALA GLU ARG ALA PHE LEU ARG HIS LEU GLU SEQRES 23 A 389 GLY GLY CYS SER VAL PRO VAL ALA VAL HIS THR ALA MET SEQRES 24 A 389 LYS ASP GLY GLN LEU TYR LEU THR GLY GLY VAL TRP SER SEQRES 25 A 389 LEU ASP GLY SER ASP SER ILE GLN GLU THR MET GLN ALA SEQRES 26 A 389 THR ILE HIS VAL PRO ALA GLN HIS GLU ASP GLY PRO GLU SEQRES 27 A 389 ASP ASP PRO GLN LEU VAL GLY ILE THR ALA ARG ASN ILE SEQRES 28 A 389 PRO ARG GLY PRO GLN LEU ALA ALA GLN ASN LEU GLY ILE SEQRES 29 A 389 SER LEU ALA ASN LEU LEU LEU SER LYS GLY ALA LYS ASN SEQRES 30 A 389 ILE LEU ASP VAL ALA ARG GLN LEU ASN ASP ALA HIS SEQRES 1 B 389 MET LYS HIS HIS HIS HIS HIS HIS PRO MET SER ASP TYR SEQRES 2 B 389 ASP ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY ALA SEQRES 3 B 389 MET ALA MET SER GLY ASN GLY ASN ALA ALA ALA THR ALA SEQRES 4 B 389 GLU GLU ASN SER PRO LYS MET ARG VAL ILE ARG VAL GLY SEQRES 5 B 389 THR ARG LYS SER GLN LEU ALA ARG ILE GLN THR ASP SER SEQRES 6 B 389 VAL VAL ALA THR LEU LYS ALA SER TYR PRO GLY LEU GLN SEQRES 7 B 389 PHE GLU ILE ILE ALA MET SER THR THR GLY ASP LYS ILE SEQRES 8 B 389 LEU ASP THR ALA LEU SER LYS ILE GLY GLU LYS SER LEU SEQRES 9 B 389 PHE THR LYS GLU LEU GLU HIS ALA LEU GLU LYS ASN GLU SEQRES 10 B 389 VAL ASP LEU VAL VAL HIS SER LEU LYS ASP LEU PRO THR SEQRES 11 B 389 VAL LEU PRO PRO GLY PHE THR ILE GLY ALA ILE CYS LYS SEQRES 12 B 389 ARG GLU ASN PRO HIS ASP ALA VAL VAL PHE HIS PRO LYS SEQRES 13 B 389 PHE VAL GLY LYS THR LEU GLU THR LEU PRO GLU LYS SER SEQRES 14 B 389 VAL VAL GLY THR SER SER LEU ARG ARG ALA ALA GLN LEU SEQRES 15 B 389 GLN ARG LYS PHE PRO HIS LEU GLU PHE ARG SER ILE ARG SEQRES 16 B 389 GLY ASN LEU ASN THR ARG LEU ARG LYS LEU ASP GLU GLN SEQRES 17 B 389 GLN GLU PHE SER ALA ILE ILE LEU ALA THR ALA GLY LEU SEQRES 18 B 389 GLN ARG MET GLY TRP HIS ASN ARG VAL GLY GLN ILE LEU SEQRES 19 B 389 HIS PRO GLU GLU CYS MET TYR ALA VAL GLY GLN GLY ALA SEQRES 20 B 389 LEU GLY VAL GLU VAL ARG ALA LYS ASP GLN ASP ILE LEU SEQRES 21 B 389 ASP LEU VAL GLY VAL LEU HIS ASP PRO GLU THR LEU LEU SEQRES 22 B 389 ARG CYS ILE ALA GLU ARG ALA PHE LEU ARG HIS LEU GLU SEQRES 23 B 389 GLY GLY CYS SER VAL PRO VAL ALA VAL HIS THR ALA MET SEQRES 24 B 389 LYS ASP GLY GLN LEU TYR LEU THR GLY GLY VAL TRP SER SEQRES 25 B 389 LEU ASP GLY SER ASP SER ILE GLN GLU THR MET GLN ALA SEQRES 26 B 389 THR ILE HIS VAL PRO ALA GLN HIS GLU ASP GLY PRO GLU SEQRES 27 B 389 ASP ASP PRO GLN LEU VAL GLY ILE THR ALA ARG ASN ILE SEQRES 28 B 389 PRO ARG GLY PRO GLN LEU ALA ALA GLN ASN LEU GLY ILE SEQRES 29 B 389 SER LEU ALA ASN LEU LEU LEU SER LYS GLY ALA LYS ASN SEQRES 30 B 389 ILE LEU ASP VAL ALA ARG GLN LEU ASN ASP ALA HIS HET 7J8 A 401 105 HET PO4 A 402 5 HET PO4 A 403 5 HET EPE A 404 32 HET 7J8 B 401 105 HET PO4 B 402 5 HETNAM 7J8 3-[4-(2-HYDROXY-2-OXOETHYL)-5-[[4-(2-HYDROXY-2- HETNAM 2 7J8 OXOETHYL)-5-[[4-(2-HYDROXY-2-OXOETHYL)-5-[[4-(2- HETNAM 3 7J8 HYDROXY-2-OXOETHYL)-3-(3-HYDROXY-3-OXOPROPYL)-5- HETNAM 4 7J8 METHYL-1~{H}-PYRROL-2-YL]METHYL]-3-(3-HYDROXY-3- HETNAM 5 7J8 OXOPROPYL)-1~{H}-PYRROL-2-YL]METHYL]-3-(3-HYDROXY-3- HETNAM 6 7J8 OXOPROPYL)-1~{H}-PYRROL-2-YL]METHYL]-1~{H}-PYRROL-3- HETNAM 7 7J8 YL]PROPANOIC ACID HETNAM PO4 PHOSPHATE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 3 7J8 2(C40 H46 N4 O16) FORMUL 4 PO4 3(O4 P 3-) FORMUL 6 EPE C8 H18 N2 O4 S FORMUL 9 HOH *23(H2 O) HELIX 1 AA1 SER A 28 TYR A 46 1 19 HELIX 2 AA2 GLY A 60 LEU A 68 1 9 HELIX 3 AA3 SER A 69 ILE A 71 5 3 HELIX 4 AA4 SER A 75 ASN A 88 1 14 HELIX 5 AA5 LYS A 98 LEU A 100 5 3 HELIX 6 AA6 THR A 133 LEU A 137 5 5 HELIX 7 AA7 SER A 147 PHE A 158 1 12 HELIX 8 AA8 ASN A 169 GLN A 180 1 12 HELIX 9 AA9 THR A 190 GLY A 197 1 8 HELIX 10 AB1 TRP A 198 VAL A 202 5 5 HELIX 11 AB2 ASP A 228 VAL A 237 1 10 HELIX 12 AB3 ASP A 240 GLU A 258 1 19 HELIX 13 AB4 PRO A 324 LYS A 345 1 22 HELIX 14 AB5 GLY A 346 LEU A 357 1 12 HELIX 15 AB6 SER B 28 TYR B 46 1 19 HELIX 16 AB7 PHE B 77 ASN B 88 1 12 HELIX 17 AB8 LYS B 98 LEU B 100 5 3 HELIX 18 AB9 THR B 133 LEU B 137 5 5 HELIX 19 AC1 SER B 147 PHE B 158 1 12 HELIX 20 AC2 ASN B 169 GLN B 180 1 12 HELIX 21 AC3 THR B 190 GLY B 197 1 8 HELIX 22 AC4 TRP B 198 VAL B 202 5 5 HELIX 23 AC5 ASP B 228 VAL B 237 1 10 HELIX 24 AC6 ASP B 240 GLU B 258 1 19 HELIX 25 AC7 PRO B 324 LYS B 345 1 22 HELIX 26 AC8 GLY B 346 VAL B 353 1 8 SHEET 1 AA1 5 PHE A 51 ALA A 55 0 SHEET 2 AA1 5 ILE A 21 THR A 25 1 N THR A 25 O ILE A 54 SHEET 3 AA1 5 LEU A 92 SER A 96 1 O LEU A 92 N GLY A 24 SHEET 4 AA1 5 LEU A 220 VAL A 224 -1 O GLY A 221 N HIS A 95 SHEET 5 AA1 5 THR A 109 ILE A 113 -1 N THR A 109 O VAL A 224 SHEET 1 AA2 4 VAL A 143 GLY A 144 0 SHEET 2 AA2 4 ALA A 185 ALA A 189 1 O ALA A 185 N GLY A 144 SHEET 3 AA2 4 ASP A 121 PHE A 125 -1 N ALA A 122 O LEU A 188 SHEET 4 AA2 4 GLN A 204 ILE A 205 -1 O GLN A 204 N VAL A 123 SHEET 1 AA3 3 VAL A 265 MET A 271 0 SHEET 2 AA3 3 LEU A 276 TRP A 283 -1 O TYR A 277 N ALA A 270 SHEET 3 AA3 3 SER A 290 ALA A 297 -1 O ALA A 297 N LEU A 276 SHEET 1 AA4 5 PHE B 51 ALA B 55 0 SHEET 2 AA4 5 ILE B 21 THR B 25 1 N VAL B 23 O GLU B 52 SHEET 3 AA4 5 LEU B 92 SER B 96 1 O LEU B 92 N GLY B 24 SHEET 4 AA4 5 LEU B 220 VAL B 224 -1 O GLY B 221 N HIS B 95 SHEET 5 AA4 5 THR B 109 ILE B 113 -1 N THR B 109 O VAL B 224 SHEET 1 AA5 5 GLU B 162 ARG B 164 0 SHEET 2 AA5 5 VAL B 142 GLY B 144 1 N VAL B 143 O GLU B 162 SHEET 3 AA5 5 ALA B 185 ALA B 189 1 O ALA B 185 N GLY B 144 SHEET 4 AA5 5 ASP B 121 PHE B 125 -1 N ALA B 122 O LEU B 188 SHEET 5 AA5 5 GLN B 204 ILE B 205 -1 O GLN B 204 N VAL B 123 SHEET 1 AA6 3 VAL B 265 MET B 271 0 SHEET 2 AA6 3 LEU B 276 TRP B 283 -1 O TYR B 277 N ALA B 270 SHEET 3 AA6 3 SER B 290 ALA B 297 -1 O ALA B 297 N LEU B 276 LINK SG CYS A 261 C 7J8 A 401 1555 1555 1.87 LINK SG CYS B 261 C 7J8 B 401 1555 1555 1.79 SITE 1 AC1 24 GLY A 72 GLU A 73 SER A 96 LYS A 98 SITE 2 AC1 24 ASP A 99 LEU A 100 PRO A 101 THR A 102 SITE 3 AC1 24 SER A 146 SER A 147 ARG A 149 ARG A 150 SITE 4 AC1 24 ARG A 173 ALA A 189 ARG A 195 ALA A 214 SITE 5 AC1 24 VAL A 215 GLN A 217 GLY A 218 LEU A 254 SITE 6 AC1 24 GLY A 260 CYS A 261 SER A 262 HOH A 509 SITE 1 AC2 4 ARG A 26 HIS A 95 SER A 96 ASP A 99 SITE 1 AC3 7 PRO A 47 GLY A 48 LEU A 49 GLN A 50 SITE 2 AC3 7 HIS B 126 LYS B 128 GLN B 181 SITE 1 AC4 4 HIS A 120 PRO A 208 GLU A 209 HIS A 268 SITE 1 AC5 5 ARG B 26 GLN B 34 HIS B 95 SER B 96 SITE 2 AC5 5 ASP B 99 SITE 1 AC6 22 SER B 96 LYS B 98 ASP B 99 LEU B 100 SITE 2 AC6 22 PRO B 101 THR B 102 SER B 146 SER B 147 SITE 3 AC6 22 ARG B 149 ARG B 150 ARG B 173 ALA B 189 SITE 4 AC6 22 ARG B 195 ALA B 214 VAL B 215 GLN B 217 SITE 5 AC6 22 GLY B 218 LEU B 254 GLY B 259 GLY B 260 SITE 6 AC6 22 SER B 262 HOH B 504 CRYST1 68.910 81.200 79.690 90.00 93.01 90.00 P 1 21 1 4 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 0.014512 0.000000 0.000763 0.00000 SCALE2 0.000000 0.012315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012566 0.00000