HEADER HYDROLASE 07-JAN-19 6QED TITLE CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; TITLE 2 WITH AN INHIBITOR (S)-3-HYDROXY-2-OXO-1-(2-OXO-1,2,3,4-TETRAHYDRO- TITLE 3 QUINOLIN-6-YL)-PYRROLIDINE-3-CARBOXYLIC ACID 3-CHLORO-5-FLUORO- TITLE 4 BENZYLAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE AMINOPEPTIDASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: METAP 2,INITIATION FACTOR 2-ASSOCIATED 67 KDA GLYCOPROTEIN, COMPND 5 P67EIF2,PEPTIDASE M; 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: METAP2, MNPEP, P67EIF2; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS HYDROLASE, PEPTIDASE, METAL ION BINDING, PROTEOLYSIS, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.MUSIL,T.HEINRICH,M.LEHMANN REVDAT 3 15-MAY-24 6QED 1 LINK REVDAT 2 05-JUN-19 6QED 1 JRNL REVDAT 1 01-MAY-19 6QED 0 JRNL AUTH T.HEINRICH,J.SEENISAMY,B.BLUME,J.BOMKE,M.CALDERINI,U.ECKERT, JRNL AUTH 2 M.FRIESE-HAMIM,R.KOHL,M.LEHMANN,B.LEUTHNER,D.MUSIL, JRNL AUTH 3 F.ROHDICH,F.T.ZENKE JRNL TITL DISCOVERY AND STRUCTURE-BASED OPTIMIZATION OF JRNL TITL 2 NEXT-GENERATION REVERSIBLE METHIONINE AMINOPEPTIDASE-2 JRNL TITL 3 (METAP-2) INHIBITORS. JRNL REF J.MED.CHEM. V. 62 5025 2019 JRNL REFN ISSN 0022-2623 JRNL PMID 30939017 JRNL DOI 10.1021/ACS.JMEDCHEM.9B00041 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 42071 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2104 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 : 50 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.00 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 842 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2257 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 800 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE : 0.2402 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.99 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2856 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 224 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.67620 REMARK 3 B22 (A**2) : 5.46370 REMARK 3 B33 (A**2) : 2.21250 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) : 0.220 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.107 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.099 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.103 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.097 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 : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3000 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4062 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1045 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 510 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3000 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 4 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 391 ; 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 : 3650 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.03 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.72 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.01 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 22.9998 24.6048 14.0862 REMARK 3 T TENSOR REMARK 3 T11: -0.1611 T22: -0.1687 REMARK 3 T33: -0.0055 T12: -0.0123 REMARK 3 T13: 0.0297 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.4928 L22: 3.5763 REMARK 3 L33: 1.0095 L12: -0.4635 REMARK 3 L13: -0.0585 L23: 0.9975 REMARK 3 S TENSOR REMARK 3 S11: 0.1313 S12: 0.0208 S13: 0.1055 REMARK 3 S21: -0.1373 S22: 0.0451 S23: -0.7848 REMARK 3 S31: -0.1085 S32: 0.0331 S33: -0.1764 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6QED COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1292100049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42072 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 44.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.47100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% METHANOL, 0.1 M CITRATE, PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.54000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.54000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 44.65000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.83500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.65000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.83500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 50.54000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 44.65000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.83500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 50.54000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 44.65000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.83500 REMARK 290 SMTRY3 8 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: 1060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 9.0 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 107 REMARK 465 GLY A 108 REMARK 465 PRO A 109 REMARK 465 LYS A 110 REMARK 465 ASP A 476 REMARK 465 ASP A 477 REMARK 465 TYR A 478 REMARK 465 HIS A 479 REMARK 465 HIS A 480 REMARK 465 HIS A 481 REMARK 465 HIS A 482 REMARK 465 HIS A 483 REMARK 465 HIS A 484 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 SER A 117 -15.83 -141.42 REMARK 500 CYS A 223 41.46 -140.07 REMARK 500 ASN A 226 -118.15 57.96 REMARK 500 MET A 378 -170.07 70.22 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 MN A 508 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 251 OD1 REMARK 620 2 ASP A 251 OD2 59.6 REMARK 620 3 ASP A 262 OD1 100.3 159.5 REMARK 620 4 GLU A 459 OE1 104.4 100.8 87.5 REMARK 620 5 HZK A 506 O14 138.1 81.0 117.1 95.7 REMARK 620 6 HZK A 506 O18 87.7 78.3 98.4 165.4 69.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 507 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 262 OD2 REMARK 620 2 HIS A 331 NE2 88.4 REMARK 620 3 GLU A 364 OE2 164.4 88.5 REMARK 620 4 GLU A 459 OE2 83.2 122.9 85.7 REMARK 620 5 HZK A 506 O14 108.0 141.6 83.6 94.0 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 EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HZK A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 508 DBREF 6QED A 108 478 UNP P50579 MAP2_HUMAN 108 478 SEQADV 6QED MET A 107 UNP P50579 INITIATING METHIONINE SEQADV 6QED HIS A 479 UNP P50579 EXPRESSION TAG SEQADV 6QED HIS A 480 UNP P50579 EXPRESSION TAG SEQADV 6QED HIS A 481 UNP P50579 EXPRESSION TAG SEQADV 6QED HIS A 482 UNP P50579 EXPRESSION TAG SEQADV 6QED HIS A 483 UNP P50579 EXPRESSION TAG SEQADV 6QED HIS A 484 UNP P50579 EXPRESSION TAG SEQRES 1 A 378 MET GLY PRO LYS VAL GLN THR ASP PRO PRO SER VAL PRO SEQRES 2 A 378 ILE CYS ASP LEU TYR PRO ASN GLY VAL PHE PRO LYS GLY SEQRES 3 A 378 GLN GLU CYS GLU TYR PRO PRO THR GLN ASP GLY ARG THR SEQRES 4 A 378 ALA ALA TRP ARG THR THR SER GLU GLU LYS LYS ALA LEU SEQRES 5 A 378 ASP GLN ALA SER GLU GLU ILE TRP ASN ASP PHE ARG GLU SEQRES 6 A 378 ALA ALA GLU ALA HIS ARG GLN VAL ARG LYS TYR VAL MET SEQRES 7 A 378 SER TRP ILE LYS PRO GLY MET THR MET ILE GLU ILE CYS SEQRES 8 A 378 GLU LYS LEU GLU ASP CYS SER ARG LYS LEU ILE LYS GLU SEQRES 9 A 378 ASN GLY LEU ASN ALA GLY LEU ALA PHE PRO THR GLY CYS SEQRES 10 A 378 SER LEU ASN ASN CYS ALA ALA HIS TYR THR PRO ASN ALA SEQRES 11 A 378 GLY ASP THR THR VAL LEU GLN TYR ASP ASP ILE CYS LYS SEQRES 12 A 378 ILE ASP PHE GLY THR HIS ILE SER GLY ARG ILE ILE ASP SEQRES 13 A 378 CYS ALA PHE THR VAL THR PHE ASN PRO LYS TYR ASP THR SEQRES 14 A 378 LEU LEU LYS ALA VAL LYS ASP ALA THR ASN THR GLY ILE SEQRES 15 A 378 LYS CYS ALA GLY ILE ASP VAL ARG LEU CYS ASP VAL GLY SEQRES 16 A 378 GLU ALA ILE GLN GLU VAL MET GLU SER TYR GLU VAL GLU SEQRES 17 A 378 ILE ASP GLY LYS THR TYR GLN VAL LYS PRO ILE ARG ASN SEQRES 18 A 378 LEU ASN GLY HIS SER ILE GLY GLN TYR ARG ILE HIS ALA SEQRES 19 A 378 GLY LYS THR VAL PRO ILE VAL LYS GLY GLY GLU ALA THR SEQRES 20 A 378 ARG MET GLU GLU GLY GLU VAL TYR ALA ILE GLU THR PHE SEQRES 21 A 378 GLY SER THR GLY LYS GLY VAL VAL HIS ASP ASP MET GLU SEQRES 22 A 378 CYS SER HIS TYR MET LYS ASN PHE ASP VAL GLY HIS VAL SEQRES 23 A 378 PRO ILE ARG LEU PRO ARG THR LYS HIS LEU LEU ASN VAL SEQRES 24 A 378 ILE ASN GLU ASN PHE GLY THR LEU ALA PHE CYS ARG ARG SEQRES 25 A 378 TRP LEU ASP ARG LEU GLY GLU SER LYS TYR LEU MET ALA SEQRES 26 A 378 LEU LYS ASN LEU CYS ASP LEU GLY ILE VAL ASP PRO TYR SEQRES 27 A 378 PRO PRO LEU CYS ASP ILE LYS GLY SER TYR THR ALA GLN SEQRES 28 A 378 PHE GLU HIS THR ILE LEU LEU ARG PRO THR CYS LYS GLU SEQRES 29 A 378 VAL VAL SER ARG GLY ASP ASP TYR HIS HIS HIS HIS HIS SEQRES 30 A 378 HIS HET EDO A 501 4 HET EDO A 502 4 HET EDO A 503 4 HET DMS A 504 4 HET GOL A 505 12 HET HZK A 506 30 HET MN A 507 1 HET MN A 508 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETNAM GOL GLYCEROL HETNAM HZK (3~{S})-~{N}-[(3-CHLORANYL-5-FLUORANYL-PHENYL)METHYL]- HETNAM 2 HZK 3-OXIDANYL-2-OXIDANYLIDENE-1-(2-OXIDANYLIDENE-3,4- HETNAM 3 HZK DIHYDRO-1~{H}-QUINOLIN-6-YL)PYRROLIDINE-3-CARBOXAMIDE HETNAM MN MANGANESE (II) ION HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 EDO 3(C2 H6 O2) FORMUL 5 DMS C2 H6 O S FORMUL 6 GOL C3 H8 O3 FORMUL 7 HZK C21 H19 CL F N3 O4 FORMUL 8 MN 2(MN 2+) FORMUL 10 HOH *224(H2 O) HELIX 1 AA1 PRO A 119 TYR A 124 1 6 HELIX 2 AA2 ALA A 147 SER A 152 1 6 HELIX 3 AA3 SER A 152 SER A 162 1 11 HELIX 4 AA4 SER A 162 ILE A 187 1 26 HELIX 5 AA5 THR A 192 LYS A 209 1 18 HELIX 6 AA6 ASN A 211 LEU A 213 5 3 HELIX 7 AA7 ASN A 270 LYS A 272 5 3 HELIX 8 AA8 TYR A 273 ALA A 291 1 19 HELIX 9 AA9 ARG A 296 GLU A 309 1 14 HELIX 10 AB1 LEU A 396 PHE A 410 1 15 HELIX 11 AB2 ARG A 417 LEU A 423 1 7 HELIX 12 AB3 TYR A 428 LEU A 438 1 11 SHEET 1 AA1 5 GLN A 133 CYS A 135 0 SHEET 2 AA1 5 LYS A 469 VAL A 471 -1 O LYS A 469 N CYS A 135 SHEET 3 AA1 5 THR A 455 LEU A 464 -1 N LEU A 463 O GLU A 470 SHEET 4 AA1 5 VAL A 360 SER A 368 -1 N ILE A 363 O HIS A 460 SHEET 5 AA1 5 LYS A 323 PRO A 324 -1 N LYS A 323 O SER A 368 SHEET 1 AA2 6 GLN A 133 CYS A 135 0 SHEET 2 AA2 6 LYS A 469 VAL A 471 -1 O LYS A 469 N CYS A 135 SHEET 3 AA2 6 THR A 455 LEU A 464 -1 N LEU A 463 O GLU A 470 SHEET 4 AA2 6 VAL A 360 SER A 368 -1 N ILE A 363 O HIS A 460 SHEET 5 AA2 6 GLY A 330 ILE A 333 -1 N HIS A 331 O ALA A 362 SHEET 6 AA2 6 THR A 343 VAL A 344 -1 O VAL A 344 N GLY A 330 SHEET 1 AA3 3 ALA A 215 LEU A 225 0 SHEET 2 AA3 3 CYS A 248 ILE A 256 -1 O ASP A 251 N GLY A 222 SHEET 3 AA3 3 ARG A 259 VAL A 267 -1 O VAL A 267 N CYS A 248 SHEET 1 AA4 3 CYS A 228 ALA A 230 0 SHEET 2 AA4 3 LEU A 447 CYS A 448 -1 O LEU A 447 N ALA A 229 SHEET 3 AA4 3 HIS A 375 ASP A 376 -1 N HIS A 375 O CYS A 448 SHEET 1 AA5 2 GLU A 312 ILE A 315 0 SHEET 2 AA5 2 LYS A 318 GLN A 321 -1 O TYR A 320 N VAL A 313 SHEET 1 AA6 3 PHE A 415 CYS A 416 0 SHEET 2 AA6 3 HIS A 382 LYS A 385 -1 N TYR A 383 O PHE A 415 SHEET 3 AA6 3 VAL A 441 TYR A 444 -1 O TYR A 444 N HIS A 382 LINK OD1 ASP A 251 MN MN A 508 1555 1555 2.16 LINK OD2 ASP A 251 MN MN A 508 1555 1555 2.25 LINK OD2 ASP A 262 MN MN A 507 1555 1555 2.07 LINK OD1 ASP A 262 MN MN A 508 1555 1555 2.02 LINK NE2 HIS A 331 MN MN A 507 1555 1555 2.24 LINK OE2 GLU A 364 MN MN A 507 1555 1555 2.16 LINK OE2 GLU A 459 MN MN A 507 1555 1555 2.20 LINK OE1 GLU A 459 MN MN A 508 1555 1555 2.14 LINK O14 HZK A 506 MN MN A 507 1555 1555 2.40 LINK O14 HZK A 506 MN MN A 508 1555 1555 2.25 LINK O18 HZK A 506 MN MN A 508 1555 1555 2.46 CISPEP 1 ASP A 114 PRO A 115 0 3.86 SITE 1 AC1 6 MET A 184 THR A 266 VAL A 267 THR A 268 SITE 2 AC1 6 LEU A 277 HOH A 634 SITE 1 AC2 2 TYR A 383 LEU A 429 SITE 1 AC3 9 ARG A 180 CYS A 263 ALA A 264 PHE A 265 SITE 2 AC3 9 PHE A 458 GLU A 459 HIS A 460 GOL A 505 SITE 3 AC3 9 HOH A 688 SITE 1 AC4 3 PRO A 443 TYR A 444 HOH A 743 SITE 1 AC5 5 ARG A 180 HIS A 460 ARG A 474 EDO A 503 SITE 2 AC5 5 HOH A 728 SITE 1 AC6 18 PHE A 219 ALA A 230 HIS A 231 ASP A 251 SITE 2 AC6 18 ASP A 262 LEU A 328 ASN A 329 HIS A 331 SITE 3 AC6 18 ILE A 338 HIS A 339 GLU A 364 HIS A 382 SITE 4 AC6 18 ALA A 414 TYR A 444 LEU A 447 GLU A 459 SITE 5 AC6 18 MN A 507 MN A 508 SITE 1 AC7 6 ASP A 262 HIS A 331 GLU A 364 GLU A 459 SITE 2 AC7 6 HZK A 506 MN A 508 SITE 1 AC8 5 ASP A 251 ASP A 262 GLU A 459 HZK A 506 SITE 2 AC8 5 MN A 507 CRYST1 89.300 99.670 101.080 90.00 90.00 90.00 C 2 2 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 0.011198 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010033 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009893 0.00000