HEADER HYDROLASE 20-SEP-05 2B3H TITLE CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE TYPE I WITH A TITLE 2 THIRD COBALT IN THE ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE AMINOPEPTIDASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 81-384; COMPND 5 SYNONYM: METAP 1, MAP 1, PEPTIDASE M 1; COMPND 6 EC: 3.4.11.18; 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: METAP1, KIAA0094; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS METHIONINE AMINOPEPTIDASE, HYDROLASE, METALLOPROTEASE, PITABREAD FOLD EXPDTA X-RAY DIFFRACTION AUTHOR A.ADDLAGATTA,X.HU,J.O.LIU,B.W.MATTHEWS REVDAT 5 23-AUG-23 2B3H 1 REMARK SEQADV LINK REVDAT 4 11-OCT-17 2B3H 1 REMARK REVDAT 3 13-JUL-11 2B3H 1 VERSN REVDAT 2 24-FEB-09 2B3H 1 VERSN REVDAT 1 22-NOV-05 2B3H 0 JRNL AUTH A.ADDLAGATTA,X.HU,J.O.LIU,B.W.MATTHEWS JRNL TITL STRUCTURAL BASIS FOR THE FUNCTIONAL DIFFERENCES BETWEEN TYPE JRNL TITL 2 I AND TYPE II HUMAN METHIONINE AMINOPEPTIDASES(,). JRNL REF BIOCHEMISTRY V. 44 14741 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 16274222 JRNL DOI 10.1021/BI051691K REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.101 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.098 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.131 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 7151 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 255244 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2396 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 511 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2B3H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 142947 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 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 (%) : 91.8 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 60.3700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.19700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR 2.5 REMARK 200 STARTING MODEL: PDB ENTRY 1YJ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2000, POTASSIUM CHLORIDE, HEPES, REMARK 280 SODIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 38.65000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 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 65 REMARK 465 GLY A 66 REMARK 465 SER A 67 REMARK 465 SER A 68 REMARK 465 HIS A 69 REMARK 465 HIS A 70 REMARK 465 HIS A 71 REMARK 465 HIS A 72 REMARK 465 HIS A 73 REMARK 465 HIS A 74 REMARK 465 SER A 75 REMARK 465 SER A 76 REMARK 465 GLY A 77 REMARK 465 LEU A 78 REMARK 465 VAL A 79 REMARK 465 PRO A 80 REMARK 465 ARG A 81 REMARK 465 GLY A 82 REMARK 465 SER A 83 REMARK 465 HIS A 84 REMARK 465 MET A 85 REMARK 465 LEU A 86 REMARK 465 GLU A 87 REMARK 465 ASP A 88 REMARK 465 PRO A 89 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CL CL A 406 O HOH A 510 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 O ALA A 130 NZ LYS A 167 1554 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO A 121 C PRO A 121 O 0.139 REMARK 500 GLU A 143 CD GLU A 143 OE2 0.082 REMARK 500 GLU A 341 CB GLU A 341 CG -0.138 REMARK 500 GLU A 341 CD GLU A 341 OE1 0.074 REMARK 500 SER A 393 C SER A 393 OXT 0.543 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 ARG A 91 CB - CG - CD ANGL. DEV. = 18.7 DEGREES REMARK 500 ARG A 91 CD - NE - CZ ANGL. DEV. = 30.9 DEGREES REMARK 500 ARG A 91 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 PRO A 104 N - CD - CG ANGL. DEV. = 11.6 DEGREES REMARK 500 PRO A 104 O - C - N ANGL. DEV. = -10.5 DEGREES REMARK 500 ARG A 106 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 PRO A 121 O - C - N ANGL. DEV. = -13.2 DEGREES REMARK 500 GLU A 126 CG - CD - OE2 ANGL. DEV. = 13.7 DEGREES REMARK 500 THR A 134 CA - CB - CG2 ANGL. DEV. = -10.3 DEGREES REMARK 500 LYS A 138 CG - CD - CE ANGL. DEV. = 18.8 DEGREES REMARK 500 GLU A 143 CB - CG - CD ANGL. DEV. = 20.4 DEGREES REMARK 500 GLU A 146 OE1 - CD - OE2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG A 149 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 149 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 153 NE - CZ - NH1 ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG A 153 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 MET A 165 CA - CB - CG ANGL. DEV. = -15.8 DEGREES REMARK 500 MET A 165 CA - CB - CG ANGL. DEV. = 16.2 DEGREES REMARK 500 GLU A 174 OE1 - CD - OE2 ANGL. DEV. = -9.2 DEGREES REMARK 500 GLU A 174 CG - CD - OE1 ANGL. DEV. = 12.9 DEGREES REMARK 500 CYS A 183 N - CA - CB ANGL. DEV. = -14.2 DEGREES REMARK 500 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 234 CD - NE - CZ ANGL. DEV. = 22.5 DEGREES REMARK 500 ARG A 255 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 255 NE - CZ - NH2 ANGL. DEV. = 8.4 DEGREES REMARK 500 MET A 266 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 ARG A 277 NH1 - CZ - NH2 ANGL. DEV. = -8.6 DEGREES REMARK 500 ARG A 277 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 277 NE - CZ - NH2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 279 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 279 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 279 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 PRO A 313 N - CD - CG ANGL. DEV. = 9.0 DEGREES REMARK 500 TRP A 344 CE3 - CZ3 - CH2 ANGL. DEV. = -10.5 DEGREES REMARK 500 THR A 375 CA - CB - OG1 ANGL. DEV. = -14.2 DEGREES REMARK 500 CYS A 377 N - CA - CB ANGL. DEV. = -18.4 DEGREES REMARK 500 CYS A 377 N - CA - CB ANGL. DEV. = 13.7 DEGREES REMARK 500 CYS A 377 CA - CB - SG ANGL. DEV. = 8.2 DEGREES REMARK 500 MET A 392 CA - CB - CG ANGL. DEV. = 12.8 DEGREES REMARK 500 SER A 393 CB - CA - C ANGL. DEV. = 14.8 DEGREES REMARK 500 SER A 393 N - CA - C ANGL. DEV. = -19.5 DEGREES REMARK 500 SER A 393 CA - C - O ANGL. DEV. = -17.8 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 ASN A 207 -115.08 51.63 REMARK 500 HIS A 306 -106.56 -174.72 REMARK 500 GLU A 336 56.54 -148.96 REMARK 500 TRP A 353 -50.95 -128.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET A 392 SER A 393 -149.99 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 K A 405 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 205 O REMARK 620 2 ASN A 207 O 126.2 REMARK 620 3 VAL A 209 O 97.1 83.6 REMARK 620 4 SER A 363 O 149.9 73.8 108.3 REMARK 620 5 HOH A 508 O 88.3 145.4 89.5 76.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 403 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 212 NE2 REMARK 620 2 GOL A 471 O1 97.0 REMARK 620 3 GOL A 471 O3 115.2 50.9 REMARK 620 4 HOH A 934 O 94.4 101.2 139.6 REMARK 620 5 HOH A 935 O 84.2 175.3 124.5 83.2 REMARK 620 6 HOH A 936 O 91.0 106.5 59.9 150.9 68.9 REMARK 620 7 HOH A 937 O 176.3 81.0 61.1 89.0 97.6 86.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 404 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 212 NE2 REMARK 620 2 HOH A 933 O 174.2 REMARK 620 3 HOH A 935 O 94.3 87.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 402 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 229 OD1 REMARK 620 2 ASP A 229 OD2 55.9 REMARK 620 3 ASP A 240 OD1 99.4 154.9 REMARK 620 4 GLU A 367 OE1 96.2 98.0 88.2 REMARK 620 5 HOH A 505 O 87.4 88.1 86.4 173.9 REMARK 620 6 HOH A 510 O 147.9 92.3 111.9 92.0 87.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 401 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 240 OD2 REMARK 620 2 HIS A 303 NE2 90.2 REMARK 620 3 GLU A 336 OE1 164.2 88.2 REMARK 620 4 GLU A 367 OE2 88.3 129.8 80.7 REMARK 620 5 HOH A 510 O 96.5 126.6 97.1 103.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 470 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 471 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B3K RELATED DB: PDB REMARK 900 RELATED ID: 2B3L RELATED DB: PDB DBREF 2B3H A 90 393 UNP P53582 AMPM1_HUMAN 81 384 SEQADV 2B3H MET A 65 UNP P53582 CLONING ARTIFACT SEQADV 2B3H GLY A 66 UNP P53582 CLONING ARTIFACT SEQADV 2B3H SER A 67 UNP P53582 CLONING ARTIFACT SEQADV 2B3H SER A 68 UNP P53582 CLONING ARTIFACT SEQADV 2B3H HIS A 69 UNP P53582 EXPRESSION TAG SEQADV 2B3H HIS A 70 UNP P53582 EXPRESSION TAG SEQADV 2B3H HIS A 71 UNP P53582 EXPRESSION TAG SEQADV 2B3H HIS A 72 UNP P53582 EXPRESSION TAG SEQADV 2B3H HIS A 73 UNP P53582 EXPRESSION TAG SEQADV 2B3H HIS A 74 UNP P53582 EXPRESSION TAG SEQADV 2B3H SER A 75 UNP P53582 CLONING ARTIFACT SEQADV 2B3H SER A 76 UNP P53582 CLONING ARTIFACT SEQADV 2B3H GLY A 77 UNP P53582 CLONING ARTIFACT SEQADV 2B3H LEU A 78 UNP P53582 CLONING ARTIFACT SEQADV 2B3H VAL A 79 UNP P53582 CLONING ARTIFACT SEQADV 2B3H PRO A 80 UNP P53582 CLONING ARTIFACT SEQADV 2B3H ARG A 81 UNP P53582 CLONING ARTIFACT SEQADV 2B3H GLY A 82 UNP P53582 CLONING ARTIFACT SEQADV 2B3H SER A 83 UNP P53582 CLONING ARTIFACT SEQADV 2B3H HIS A 84 UNP P53582 CLONING ARTIFACT SEQADV 2B3H MET A 85 UNP P53582 CLONING ARTIFACT SEQADV 2B3H LEU A 86 UNP P53582 CLONING ARTIFACT SEQADV 2B3H GLU A 87 UNP P53582 CLONING ARTIFACT SEQADV 2B3H ASP A 88 UNP P53582 CLONING ARTIFACT SEQADV 2B3H PRO A 89 UNP P53582 CLONING ARTIFACT SEQRES 1 A 329 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 329 LEU VAL PRO ARG GLY SER HIS MET LEU GLU ASP PRO TYR SEQRES 3 A 329 ARG TYR THR GLY LYS LEU ARG PRO HIS TYR PRO LEU MET SEQRES 4 A 329 PRO THR ARG PRO VAL PRO SER TYR ILE GLN ARG PRO ASP SEQRES 5 A 329 TYR ALA ASP HIS PRO LEU GLY MET SER GLU SER GLU GLN SEQRES 6 A 329 ALA LEU LYS GLY THR SER GLN ILE LYS LEU LEU SER SER SEQRES 7 A 329 GLU ASP ILE GLU GLY MET ARG LEU VAL CYS ARG LEU ALA SEQRES 8 A 329 ARG GLU VAL LEU ASP VAL ALA ALA GLY MET ILE LYS PRO SEQRES 9 A 329 GLY VAL THR THR GLU GLU ILE ASP HIS ALA VAL HIS LEU SEQRES 10 A 329 ALA CYS ILE ALA ARG ASN CYS TYR PRO SER PRO LEU ASN SEQRES 11 A 329 TYR TYR ASN PHE PRO LYS SER CYS CYS THR SER VAL ASN SEQRES 12 A 329 GLU VAL ILE CYS HIS GLY ILE PRO ASP ARG ARG PRO LEU SEQRES 13 A 329 GLN GLU GLY ASP ILE VAL ASN VAL ASP ILE THR LEU TYR SEQRES 14 A 329 ARG ASN GLY TYR HIS GLY ASP LEU ASN GLU THR PHE PHE SEQRES 15 A 329 VAL GLY GLU VAL ASP ASP GLY ALA ARG LYS LEU VAL GLN SEQRES 16 A 329 THR THR TYR GLU CYS LEU MET GLN ALA ILE ASP ALA VAL SEQRES 17 A 329 LYS PRO GLY VAL ARG TYR ARG GLU LEU GLY ASN ILE ILE SEQRES 18 A 329 GLN LYS HIS ALA GLN ALA ASN GLY PHE SER VAL VAL ARG SEQRES 19 A 329 SER TYR CYS GLY HIS GLY ILE HIS LYS LEU PHE HIS THR SEQRES 20 A 329 ALA PRO ASN VAL PRO HIS TYR ALA LYS ASN LYS ALA VAL SEQRES 21 A 329 GLY VAL MET LYS SER GLY HIS VAL PHE THR ILE GLU PRO SEQRES 22 A 329 MET ILE CYS GLU GLY GLY TRP GLN ASP GLU THR TRP PRO SEQRES 23 A 329 ASP GLY TRP THR ALA VAL THR ARG ASP GLY LYS ARG SER SEQRES 24 A 329 ALA GLN PHE GLU HIS THR LEU LEU VAL THR ASP THR GLY SEQRES 25 A 329 CYS GLU ILE LEU THR ARG ARG LEU ASP SER ALA ARG PRO SEQRES 26 A 329 HIS PHE MET SER HET CO A 401 1 HET CO A 402 1 HET K A 405 1 HET CL A 406 1 HET CO A 403 1 HET CO A 404 1 HET GOL A 470 12 HET GOL A 471 6 HETNAM CO COBALT (II) ION HETNAM K POTASSIUM ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CO 4(CO 2+) FORMUL 4 K K 1+ FORMUL 5 CL CL 1- FORMUL 8 GOL 2(C3 H8 O3) FORMUL 10 HOH *511(H2 O) HELIX 1 1 PRO A 115 HIS A 120 5 6 HELIX 2 2 SER A 125 LEU A 131 1 7 HELIX 3 3 SER A 141 MET A 165 1 25 HELIX 4 4 THR A 171 ARG A 186 1 16 HELIX 5 5 ASN A 194 PHE A 198 5 5 HELIX 6 6 ASP A 251 ALA A 271 1 21 HELIX 7 7 ARG A 279 ASN A 292 1 14 HELIX 8 8 PRO A 389 SER A 393 5 5 SHEET 1 A 3 TYR A 189 PRO A 190 0 SHEET 2 A 3 ILE A 225 ARG A 234 -1 O TYR A 233 N TYR A 189 SHEET 3 A 3 CYS A 203 VAL A 206 -1 N SER A 205 O ASN A 227 SHEET 1 B 3 TYR A 189 PRO A 190 0 SHEET 2 B 3 ILE A 225 ARG A 234 -1 O TYR A 233 N TYR A 189 SHEET 3 B 3 TYR A 237 PHE A 246 -1 O PHE A 245 N VAL A 226 SHEET 1 C 3 VAL A 209 CYS A 211 0 SHEET 2 C 3 ALA A 355 THR A 357 -1 O ALA A 355 N CYS A 211 SHEET 3 C 3 ASP A 346 THR A 348 -1 N GLU A 347 O VAL A 356 SHEET 1 D 3 SER A 295 VAL A 296 0 SHEET 2 D 3 MET A 338 CYS A 340 -1 O CYS A 340 N SER A 295 SHEET 3 D 3 SER A 363 GLN A 365 -1 O ALA A 364 N ILE A 339 SHEET 1 E 2 GLY A 302 GLY A 304 0 SHEET 2 E 2 THR A 311 VAL A 315 -1 O VAL A 315 N GLY A 302 SHEET 1 F 3 VAL A 332 ILE A 335 0 SHEET 2 F 3 HIS A 368 VAL A 372 -1 O LEU A 370 N PHE A 333 SHEET 3 F 3 CYS A 377 ILE A 379 -1 O GLU A 378 N LEU A 371 LINK O SER A 205 K K A 405 1555 1555 2.99 LINK O ASN A 207 K K A 405 1555 1555 2.86 LINK O VAL A 209 K K A 405 1555 1555 2.63 LINK NE2 HIS A 212 CO CO A 403 1555 1555 2.15 LINK NE2 HIS A 212 CO CO A 404 1555 1555 2.01 LINK OD1 ASP A 229 CO CO A 402 1555 1555 2.09 LINK OD2 ASP A 229 CO CO A 402 1555 1555 2.38 LINK OD2 ASP A 240 CO CO A 401 1555 1555 2.11 LINK OD1 ASP A 240 CO CO A 402 1555 1555 2.01 LINK NE2 HIS A 303 CO CO A 401 1555 1555 2.04 LINK OE1 GLU A 336 CO CO A 401 1555 1555 2.19 LINK O SER A 363 K K A 405 1555 1555 2.67 LINK OE2 GLU A 367 CO CO A 401 1555 1555 2.00 LINK OE1 GLU A 367 CO CO A 402 1555 1555 2.12 LINK CO CO A 401 O HOH A 510 1555 1555 1.97 LINK CO CO A 402 O HOH A 505 1555 1555 2.21 LINK CO CO A 402 O HOH A 510 1555 1555 2.02 LINK CO CO A 403 O1 GOL A 471 1555 1555 2.08 LINK CO CO A 403 O3 GOL A 471 1555 1555 2.12 LINK CO CO A 403 O HOH A 934 1555 1555 2.17 LINK CO CO A 403 O HOH A 935 1555 1555 2.13 LINK CO CO A 403 O HOH A 936 1555 1555 2.18 LINK CO CO A 403 O HOH A 937 1555 1555 2.31 LINK CO CO A 404 O HOH A 933 1555 1555 2.33 LINK CO CO A 404 O HOH A 935 1555 1555 1.90 LINK K K A 405 O HOH A 508 1555 1555 2.82 CISPEP 1 TYR A 100 PRO A 101 0 -0.20 CISPEP 2 ALA A 312 PRO A 313 0 5.90 SITE 1 AC1 8 ASP A 240 HIS A 303 THR A 334 GLU A 336 SITE 2 AC1 8 GLU A 367 CO A 402 CL A 406 HOH A 510 SITE 1 AC2 7 ASP A 229 ASP A 240 GLU A 367 CO A 401 SITE 2 AC2 7 CL A 406 HOH A 505 HOH A 510 SITE 1 AC3 5 SER A 205 ASN A 207 VAL A 209 SER A 363 SITE 2 AC3 5 HOH A 508 SITE 1 AC4 12 HIS A 310 CO A 401 CO A 402 CO A 403 SITE 2 AC4 12 CO A 404 GOL A 471 HOH A 505 HOH A 510 SITE 3 AC4 12 HOH A 933 HOH A 934 HOH A 935 HOH A 936 SITE 1 AC5 8 HIS A 212 CO A 404 CL A 406 GOL A 471 SITE 2 AC5 8 HOH A 934 HOH A 935 HOH A 936 HOH A 937 SITE 1 AC6 7 HIS A 212 CO A 403 CL A 406 GOL A 471 SITE 2 AC6 7 HOH A 933 HOH A 934 HOH A 935 SITE 1 AC7 11 THR A 172 THR A 204 SER A 205 VAL A 206 SITE 2 AC7 11 VAL A 209 ILE A 214 ASP A 216 ARG A 218 SITE 3 AC7 11 HOH A 502 HOH A 506 HOH A 564 SITE 1 AC8 12 PHE A 198 CYS A 203 HIS A 212 HIS A 310 SITE 2 AC8 12 TRP A 353 CO A 403 CO A 404 CL A 406 SITE 3 AC8 12 HOH A 688 HOH A 726 HOH A 936 HOH A 937 CRYST1 47.290 77.300 48.340 90.00 91.03 90.00 P 1 21 1 2 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 0.021146 0.000000 0.000380 0.00000 SCALE2 0.000000 0.012937 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020690 0.00000