HEADER HYDROLASE 18-FEB-20 6LZC TITLE CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE (HSMETAP1B) IN TITLE 2 COMPLEX WITH KV-P2-4H-05 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE AMINOPEPTIDASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: METAP 1,PEPTIDASE M 1; COMPND 5 EC: 3.4.11.18; 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 GENE: METAP1, KIAA0094; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METHIONINE AMINOPEPTIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.B.SANDEEP,A.ADDLAGATTA REVDAT 3 29-NOV-23 6LZC 1 REMARK REVDAT 2 18-AUG-21 6LZC 1 JRNL REVDAT 1 24-FEB-21 6LZC 0 JRNL AUTH S.BALA,K.V.YELLAMANDA,A.KADARI,V.S.U.RAVINUTHALA,B.KATTULA, JRNL AUTH 2 O.V.SINGH,R.GUNDLA,A.ADDLAGATTA JRNL TITL SELECTIVE INHIBITION OF HELICOBACTER PYLORI METHIONINE JRNL TITL 2 AMINOPEPTIDASE BY AZAINDOLE HYDROXAMIC ACID DERIVATIVES: JRNL TITL 3 DESIGN, SYNTHESIS, IN VITRO BIOCHEMICAL AND STRUCTURAL JRNL TITL 4 STUDIES. JRNL REF BIOORG.CHEM. V. 115 05185 2021 JRNL REFN ISSN 0045-2068 JRNL PMID 34329997 JRNL DOI 10.1016/J.BIOORG.2021.105185 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 72016 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 3636 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5263 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 294 REMARK 3 BIN FREE R VALUE : 0.2930 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 : 42 REMARK 3 SOLVENT ATOMS : 181 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.27000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.35000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.055 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.053 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.899 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2586 ; 0.017 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2351 ; 0.005 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3520 ; 2.293 ; 1.664 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5459 ; 1.605 ; 1.582 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 323 ; 7.167 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 147 ;33.340 ;20.748 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 426 ;14.492 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;14.856 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 326 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2943 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 577 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4937 ; 6.699 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6LZC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1300015577. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76213 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 47.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.72200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.7.01 REMARK 200 STARTING MODEL: 2G3H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BISTRIS PH-6.2, 19% PEG 3350, 5% REMARK 280 GLYCEROL, PH 6.2, VAPOR DIFFUSION, HANGING DROP, 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 38.60950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 MG MG A 408 O HOH A 530 1.56 REMARK 500 N EYL A 403 O HOH A 505 1.59 REMARK 500 MG MG A 408 O HOH A 619 1.66 REMARK 500 O HOH A 676 O HOH A 677 1.97 REMARK 500 O HOH A 657 O HOH A 677 2.08 REMARK 500 C14 EYL A 403 O HOH A 505 2.10 REMARK 500 OG SER A 393 O HOH A 507 2.16 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 NH2 ARG A 217 O HOH A 644 2546 2.01 REMARK 500 O ALA A 130 NZ LYS A 167 1554 2.19 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 217 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 217 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 234 CG - CD - NE ANGL. DEV. = -13.4 DEGREES REMARK 500 ARG A 234 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 CYS A 377 N - CA - CB ANGL. DEV. = -15.6 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 -116.28 50.72 REMARK 500 HIS A 306 -99.03 -175.81 REMARK 500 GLU A 336 55.39 -145.78 REMARK 500 TRP A 353 -52.09 -122.49 REMARK 500 TRP A 353 -50.07 -122.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 CYS A 183 10.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 681 DISTANCE = 6.11 ANGSTROMS 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 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 207 O REMARK 620 2 VAL A 209 O 95.7 REMARK 620 3 SER A 363 O 94.1 120.2 REMARK 620 4 HOH A 596 O 123.9 127.9 91.8 REMARK 620 5 HOH A 658 O 165.8 91.8 71.7 58.4 REMARK 620 N 1 2 3 4 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 55.5 REMARK 620 3 ASP A 240 OD1 102.9 158.4 REMARK 620 4 GLU A 367 OE1 98.7 93.6 89.8 REMARK 620 5 EYL A 403 O 87.0 80.6 99.7 167.7 REMARK 620 6 EYL A 403 N 122.3 78.3 118.5 118.4 50.0 REMARK 620 7 EYL A 403 O1 142.9 88.3 113.0 90.6 78.4 29.3 REMARK 620 8 HOH A 501 O 84.9 95.7 80.8 170.5 19.9 65.8 91.7 REMARK 620 N 1 2 3 4 5 6 7 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 90.7 REMARK 620 3 GLU A 336 OE1 156.2 85.8 REMARK 620 4 GLU A 367 OE2 83.9 122.4 78.3 REMARK 620 5 EYL A 403 O1 93.9 142.9 103.0 94.6 REMARK 620 6 HOH A 505 O 94.0 84.6 109.1 152.8 58.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 408 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 657 O REMARK 620 2 HOH A 661 O 146.5 REMARK 620 3 HOH A 676 O 87.4 61.4 REMARK 620 4 HOH A 677 O 48.5 104.5 43.8 REMARK 620 N 1 2 3 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 EYL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 408 DBREF 6LZC A 90 393 UNP P53582 MAP11_HUMAN 81 384 SEQADV 6LZC MET A 65 UNP P53582 INITIATING METHIONINE SEQADV 6LZC GLY A 66 UNP P53582 EXPRESSION TAG SEQADV 6LZC SER A 67 UNP P53582 EXPRESSION TAG SEQADV 6LZC SER A 68 UNP P53582 EXPRESSION TAG SEQADV 6LZC HIS A 69 UNP P53582 EXPRESSION TAG SEQADV 6LZC HIS A 70 UNP P53582 EXPRESSION TAG SEQADV 6LZC HIS A 71 UNP P53582 EXPRESSION TAG SEQADV 6LZC HIS A 72 UNP P53582 EXPRESSION TAG SEQADV 6LZC HIS A 73 UNP P53582 EXPRESSION TAG SEQADV 6LZC HIS A 74 UNP P53582 EXPRESSION TAG SEQADV 6LZC SER A 75 UNP P53582 EXPRESSION TAG SEQADV 6LZC SER A 76 UNP P53582 EXPRESSION TAG SEQADV 6LZC GLY A 77 UNP P53582 EXPRESSION TAG SEQADV 6LZC LEU A 78 UNP P53582 EXPRESSION TAG SEQADV 6LZC VAL A 79 UNP P53582 EXPRESSION TAG SEQADV 6LZC PRO A 80 UNP P53582 EXPRESSION TAG SEQADV 6LZC ARG A 81 UNP P53582 EXPRESSION TAG SEQADV 6LZC GLY A 82 UNP P53582 EXPRESSION TAG SEQADV 6LZC SER A 83 UNP P53582 EXPRESSION TAG SEQADV 6LZC HIS A 84 UNP P53582 EXPRESSION TAG SEQADV 6LZC MET A 85 UNP P53582 EXPRESSION TAG SEQADV 6LZC LEU A 86 UNP P53582 EXPRESSION TAG SEQADV 6LZC GLU A 87 UNP P53582 EXPRESSION TAG SEQADV 6LZC ASP A 88 UNP P53582 EXPRESSION TAG SEQADV 6LZC PRO A 89 UNP P53582 EXPRESSION TAG 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 EYL A 403 20 HET NA A 404 1 HET GOL A 405 6 HET GOL A 406 6 HET GOL A 407 6 HET MG A 408 1 HETNAM CO COBALT (II) ION HETNAM EYL ~{N}-OXIDANYL-1-(PHENYLMETHYL)PYRROLO[2,3-B]PYRIDINE-4- HETNAM 2 EYL CARBOXAMIDE HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CO 2(CO 2+) FORMUL 4 EYL C15 H13 N3 O2 FORMUL 5 NA NA 1+ FORMUL 6 GOL 3(C3 H8 O3) FORMUL 9 MG MG 2+ FORMUL 10 HOH *181(H2 O) HELIX 1 AA1 PRO A 115 HIS A 120 5 6 HELIX 2 AA2 SER A 125 LEU A 131 1 7 HELIX 3 AA3 SER A 141 GLY A 164 1 24 HELIX 4 AA4 THR A 171 ARG A 186 1 16 HELIX 5 AA5 ASN A 194 PHE A 198 5 5 HELIX 6 AA6 ASP A 251 VAL A 272 1 22 HELIX 7 AA7 ARG A 279 ASN A 292 1 14 HELIX 8 AA8 PRO A 389 SER A 393 5 5 SHEET 1 AA1 3 TYR A 189 PRO A 190 0 SHEET 2 AA1 3 ILE A 225 ARG A 234 -1 O TYR A 233 N TYR A 189 SHEET 3 AA1 3 CYS A 203 VAL A 206 -1 N SER A 205 O ASN A 227 SHEET 1 AA2 3 TYR A 189 PRO A 190 0 SHEET 2 AA2 3 ILE A 225 ARG A 234 -1 O TYR A 233 N TYR A 189 SHEET 3 AA2 3 TYR A 237 PHE A 246 -1 O LEU A 241 N ILE A 230 SHEET 1 AA3 3 VAL A 209 CYS A 211 0 SHEET 2 AA3 3 ALA A 355 THR A 357 -1 O ALA A 355 N ILE A 210 SHEET 3 AA3 3 ASP A 346 THR A 348 -1 N GLU A 347 O VAL A 356 SHEET 1 AA4 3 SER A 295 VAL A 296 0 SHEET 2 AA4 3 MET A 338 CYS A 340 -1 O CYS A 340 N SER A 295 SHEET 3 AA4 3 SER A 363 GLN A 365 -1 O ALA A 364 N ILE A 339 SHEET 1 AA5 2 GLY A 302 GLY A 304 0 SHEET 2 AA5 2 THR A 311 VAL A 315 -1 O VAL A 315 N GLY A 302 SHEET 1 AA6 3 VAL A 332 ILE A 335 0 SHEET 2 AA6 3 HIS A 368 THR A 373 -1 O LEU A 370 N PHE A 333 SHEET 3 AA6 3 GLY A 376 ILE A 379 -1 O GLU A 378 N LEU A 371 LINK O ASN A 207 NA NA A 404 1555 1555 2.29 LINK O VAL A 209 NA NA A 404 1555 1555 2.22 LINK OD1 ASP A 229 CO CO A 402 1555 1555 1.96 LINK OD2 ASP A 229 CO CO A 402 1555 1555 2.46 LINK OD2 ASP A 240 CO CO A 401 1555 1555 2.06 LINK OD1 ASP A 240 CO CO A 402 1555 1555 1.92 LINK NE2 HIS A 303 CO CO A 401 1555 1555 2.00 LINK OE1 GLU A 336 CO CO A 401 1555 1555 2.17 LINK O SER A 363 NA NA A 404 1555 1555 2.28 LINK OE2 GLU A 367 CO CO A 401 1555 1555 2.03 LINK OE1 GLU A 367 CO CO A 402 1555 1555 2.17 LINK CO CO A 401 O1 EYL A 403 1555 1555 1.99 LINK CO CO A 401 O HOH A 505 1555 1555 2.66 LINK CO CO A 402 O EYL A 403 1555 1555 2.25 LINK CO CO A 402 N EYL A 403 1555 1555 2.73 LINK CO CO A 402 O1 EYL A 403 1555 1555 1.91 LINK CO CO A 402 O HOH A 501 1555 1555 2.22 LINK NA NA A 404 O HOH A 596 1555 1555 2.35 LINK NA NA A 404 O HOH A 658 1555 1555 3.17 LINK MG MG A 408 O HOH A 657 1555 1555 2.10 LINK MG MG A 408 O HOH A 661 1555 1555 2.19 LINK MG MG A 408 O HOH A 676 1555 1555 2.47 LINK MG MG A 408 O HOH A 677 1555 1555 2.76 CISPEP 1 TYR A 100 PRO A 101 0 -0.85 CISPEP 2 ALA A 312 PRO A 313 0 1.68 SITE 1 AC1 7 ASP A 240 HIS A 303 GLU A 336 GLU A 367 SITE 2 AC1 7 CO A 402 EYL A 403 HOH A 505 SITE 1 AC2 6 ASP A 229 ASP A 240 GLU A 367 CO A 401 SITE 2 AC2 6 EYL A 403 HOH A 501 SITE 1 AC3 17 TYR A 195 HIS A 212 ASP A 229 THR A 231 SITE 2 AC3 17 ASP A 240 PHE A 309 HIS A 310 GLU A 336 SITE 3 AC3 17 TRP A 353 GLU A 367 CO A 401 CO A 402 SITE 4 AC3 17 GOL A 407 HOH A 501 HOH A 505 HOH A 534 SITE 5 AC3 17 HOH A 617 SITE 1 AC4 4 ASN A 207 VAL A 209 SER A 363 HOH A 596 SITE 1 AC5 5 ARG A 106 PRO A 107 HIS A 177 HIS A 180 SITE 2 AC5 5 LEU A 181 SITE 1 AC6 8 ALA A 163 GLY A 164 HIS A 390 SER A 393 SITE 2 AC6 8 HOH A 509 HOH A 520 HOH A 532 HOH A 541 SITE 1 AC7 4 HIS A 212 TYR A 300 HIS A 310 EYL A 403 SITE 1 AC8 7 HIS A 99 HOH A 530 HOH A 619 HOH A 657 SITE 2 AC8 7 HOH A 661 HOH A 676 HOH A 677 CRYST1 47.552 77.219 48.651 90.00 91.55 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 0.021030 0.000000 0.000569 0.00000 SCALE2 0.000000 0.012950 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020562 0.00000