HEADER HYDROLASE 22-DEC-08 3FMQ TITLE CRYSTAL STRUCTURE OF AN ENCEPHALITOZOON CUNICULI METHIONINE TITLE 2 AMINOPEPTIDASE TYPE 2 WITH ANGIOGENESIS INHIBITOR FUMAGILLIN BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE AMINOPEPTIDASE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: METAP 2, MAP-2, PEPTIDASE M 2; COMPND 5 EC: 3.4.11.18; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENCEPHALITOZOON CUNICULI; SOURCE 3 ORGANISM_TAXID: 6035; SOURCE 4 STRAIN: GB-M1; SOURCE 5 GENE: ECU10_0750, MAP2; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PBAC2 KEYWDS METHIONINE AMINOPEPTIDASE TYPE2, METAP2, METAP2 FUMAGILLIN COMPLEX, KEYWDS 2 ENCEPHALITOZOON CUNICULI, STRUCTURAL GENOMICS, PSI-2, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL KEYWDS 4 GENOMICS, NYSGXRC, AMINOPEPTIDASE, COBALT, HYDROLASE, METAL-BINDING, KEYWDS 5 PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR J.J.ALVARADO,M.RUSSELL,A.ZHANG,J.ADAMS,R.TORO,S.K.BURLEY,L.M.WEISS, AUTHOR 2 S.C.ALMO,NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS AUTHOR 3 (NYSGXRC) REVDAT 5 06-SEP-23 3FMQ 1 REMARK REVDAT 4 10-FEB-21 3FMQ 1 AUTHOR REMARK LINK REVDAT 3 01-NOV-17 3FMQ 1 REMARK REVDAT 2 22-DEC-09 3FMQ 1 JRNL REVDAT 1 13-JAN-09 3FMQ 0 SPRSDE 13-JAN-09 3FMQ 3CMK JRNL AUTH J.J.ALVARADO,A.NEMKAL,J.M.SAUDER,M.RUSSELL,D.E.AKIYOSHI, JRNL AUTH 2 W.SHI,S.C.ALMO,L.M.WEISS JRNL TITL STRUCTURE OF A MICROSPORIDIAN METHIONINE AMINOPEPTIDASE TYPE JRNL TITL 2 2 COMPLEXED WITH FUMAGILLIN AND TNP-470. JRNL REF MOL.BIOCHEM.PARASITOL. V. 168 158 2009 JRNL REFN ISSN 0166-6851 JRNL PMID 19660503 JRNL DOI 10.1016/J.MOLBIOPARA.2009.07.008 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 25385 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) : 0.173 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1286 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1401 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5514 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 227 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.56000 REMARK 3 B22 (A**2) : 1.37000 REMARK 3 B33 (A**2) : -0.81000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.180 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.289 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.200 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.980 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5697 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7722 ; 1.270 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 714 ; 6.014 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 255 ;30.363 ;23.647 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 964 ;16.138 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 43 ;20.055 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 866 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4303 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3532 ; 0.497 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5705 ; 1.005 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2165 ; 1.680 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2009 ; 2.843 ; 4.500 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): NULL ; NULL ; NULL 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 : MASK 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 REMARK 4 REMARK 4 3FMQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000050780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0809 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25402 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4440 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.29400 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.4.0069 REMARK 200 STARTING MODEL: PDB ENTRY 3FM3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG 4000, 0.2M AMMONIUM SULFATE, REMARK 280 0.5MM FUMAGILLIN. CRYOSOLUTION: 30% PEG 4000, 0.2M AMMONIUM REMARK 280 SULFATE, 10% MPD, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 47.11900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 1 REMARK 465 LYS A 2 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 8 CB CG CD OE1 NE2 REMARK 470 GLU A 10 CG CD OE1 OE2 REMARK 470 ASP A 20 CG OD1 OD2 REMARK 470 ARG A 175 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 197 NE CZ NH1 NH2 REMARK 470 ARG A 216 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 229 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 235 CD CE NZ REMARK 470 LYS A 275 CD CE NZ REMARK 470 GLU A 346 CB CG CD OE1 OE2 REMARK 470 GLN B 8 CB CG CD OE1 NE2 REMARK 470 GLU B 10 CG CD OE1 OE2 REMARK 470 LYS B 19 CD CE NZ REMARK 470 ARG B 32 CB CG CD NE CZ NH1 NH2 REMARK 470 GLU B 37 CD OE1 OE2 REMARK 470 LYS B 235 CG CD CE NZ REMARK 470 LYS B 275 CD CE NZ 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 LEU A 5 -46.79 68.19 REMARK 500 LYS A 88 127.49 -39.98 REMARK 500 ASN A 92 26.78 49.82 REMARK 500 ASN A 104 -113.81 49.82 REMARK 500 PHE A 215 13.20 58.32 REMARK 500 LEU B 5 -50.71 70.85 REMARK 500 SER B 42 165.75 178.40 REMARK 500 ASN B 104 -109.25 56.92 REMARK 500 TYR B 267 91.51 -65.73 REMARK 500 ASP B 329 -165.68 -78.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 FUMAGILLIN (FUG) FORMS A COVALENT BOND WITH HISTIDINE 109. REMARK 600 IN BOTH FUMAGILLIN MOLECULES THAT ARE PRESENT IN THE REMARK 600 ASYMMETRIC UNIT, THE FOLLOWING ATOMS ARE DISORDERED: REMARK 600 C44, C45, C46, C47, C48, C49, C4A, O4B, O4C. REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 FUG A 481 REMARK 610 FUG B 481 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 FE A 452 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 130 OD1 REMARK 620 2 ASP A 130 OD2 57.1 REMARK 620 3 ASP A 141 OD1 93.3 148.7 REMARK 620 4 GLU A 339 OE1 105.1 96.9 80.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 451 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 141 OD2 REMARK 620 2 HIS A 210 NE2 90.7 REMARK 620 3 GLU A 243 OE1 158.4 93.7 REMARK 620 4 GLU A 339 OE2 84.8 113.4 74.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 452 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 130 OD1 REMARK 620 2 ASP B 130 OD2 54.6 REMARK 620 3 ASP B 141 OD1 93.3 147.9 REMARK 620 4 GLU B 339 OE1 101.0 96.4 87.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 451 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 141 OD2 REMARK 620 2 HIS B 210 NE2 89.3 REMARK 620 3 GLU B 243 OE2 168.1 86.3 REMARK 620 4 GLU B 339 OE2 83.4 113.5 88.2 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 FE A 451 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 452 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FUG A 481 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 451 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 452 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FUG B 481 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FM3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN ENCEPHALITOZOON CUNICULI METHIONINE REMARK 900 AMINOPEPTIDASE TYPE 2, APO FORM REMARK 900 RELATED ID: 3FMR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN ENCEPHALITOZOON CUNICULI METHIONINE REMARK 900 AMINOPEPTIDASE TYPE 2 WITH ANGIOGENESIS INHIBITOR TNP470 BOUND REMARK 900 RELATED ID: NYSGXRC-9201A RELATED DB: TARGETDB DBREF 3FMQ A 1 358 UNP Q8SR45 AMPM2_ENCCU 1 358 DBREF 3FMQ B 1 358 UNP Q8SR45 AMPM2_ENCCU 1 358 SEQRES 1 A 358 MET LYS CYS ILE LEU LEU ASN GLN ALA GLU GLU LEU PRO SEQRES 2 A 358 ILE GLU PHE LEU PRO LYS ASP GLY VAL TYR GLY LYS GLY SEQRES 3 A 358 LYS LEU PHE ASP SER ARG ASN MET GLU ILE GLU ASN PHE SEQRES 4 A 358 THR GLU SER ASP ILE LEU GLN ASP ALA ARG ARG ALA ALA SEQRES 5 A 358 GLU ALA HIS ARG ARG ALA ARG TYR ARG VAL GLN SER ILE SEQRES 6 A 358 VAL ARG PRO GLY ILE THR LEU LEU GLU ILE VAL ARG SER SEQRES 7 A 358 ILE GLU ASP SER THR ARG THR LEU LEU LYS GLY GLU ARG SEQRES 8 A 358 ASN ASN GLY ILE GLY PHE PRO ALA GLY MET SER MET ASN SEQRES 9 A 358 SER CYS ALA ALA HIS TYR THR VAL ASN PRO GLY GLU GLN SEQRES 10 A 358 ASP ILE VAL LEU LYS GLU ASP ASP VAL LEU LYS ILE ASP SEQRES 11 A 358 PHE GLY THR HIS SER ASP GLY ARG ILE MET ASP SER ALA SEQRES 12 A 358 PHE THR VAL ALA PHE LYS GLU ASN LEU GLU PRO LEU LEU SEQRES 13 A 358 VAL ALA ALA ARG GLU GLY THR GLU THR GLY ILE LYS SER SEQRES 14 A 358 LEU GLY VAL ASP VAL ARG VAL CYS ASP ILE GLY ARG ASP SEQRES 15 A 358 ILE ASN GLU VAL ILE SER SER TYR GLU VAL GLU ILE GLY SEQRES 16 A 358 GLY ARG MET TRP PRO ILE ARG PRO ILE SER ASP LEU HIS SEQRES 17 A 358 GLY HIS SER ILE SER GLN PHE ARG ILE HIS GLY GLY ILE SEQRES 18 A 358 SER ILE PRO ALA VAL ASN ASN ARG ASP THR THR ARG ILE SEQRES 19 A 358 LYS GLY ASP SER PHE TYR ALA VAL GLU THR PHE ALA THR SEQRES 20 A 358 THR GLY LYS GLY SER ILE ASP ASP ARG PRO PRO CYS SER SEQRES 21 A 358 HIS PHE VAL LEU ASN THR TYR LYS SER ARG LYS LEU PHE SEQRES 22 A 358 ASN LYS ASP LEU ILE LYS VAL TYR GLU PHE VAL LYS ASP SEQRES 23 A 358 SER LEU GLY THR LEU PRO PHE SER PRO ARG HIS LEU ASP SEQRES 24 A 358 TYR TYR GLY LEU VAL LYS GLY GLY SER LEU LYS SER VAL SEQRES 25 A 358 ASN LEU LEU THR MET MET GLY LEU LEU THR PRO TYR PRO SEQRES 26 A 358 PRO LEU ASN ASP ILE ASP GLY CYS LYS VAL ALA GLN PHE SEQRES 27 A 358 GLU HIS THR VAL TYR LEU SER GLU HIS GLY LYS GLU VAL SEQRES 28 A 358 LEU THR ARG GLY ASP ASP TYR SEQRES 1 B 358 MET LYS CYS ILE LEU LEU ASN GLN ALA GLU GLU LEU PRO SEQRES 2 B 358 ILE GLU PHE LEU PRO LYS ASP GLY VAL TYR GLY LYS GLY SEQRES 3 B 358 LYS LEU PHE ASP SER ARG ASN MET GLU ILE GLU ASN PHE SEQRES 4 B 358 THR GLU SER ASP ILE LEU GLN ASP ALA ARG ARG ALA ALA SEQRES 5 B 358 GLU ALA HIS ARG ARG ALA ARG TYR ARG VAL GLN SER ILE SEQRES 6 B 358 VAL ARG PRO GLY ILE THR LEU LEU GLU ILE VAL ARG SER SEQRES 7 B 358 ILE GLU ASP SER THR ARG THR LEU LEU LYS GLY GLU ARG SEQRES 8 B 358 ASN ASN GLY ILE GLY PHE PRO ALA GLY MET SER MET ASN SEQRES 9 B 358 SER CYS ALA ALA HIS TYR THR VAL ASN PRO GLY GLU GLN SEQRES 10 B 358 ASP ILE VAL LEU LYS GLU ASP ASP VAL LEU LYS ILE ASP SEQRES 11 B 358 PHE GLY THR HIS SER ASP GLY ARG ILE MET ASP SER ALA SEQRES 12 B 358 PHE THR VAL ALA PHE LYS GLU ASN LEU GLU PRO LEU LEU SEQRES 13 B 358 VAL ALA ALA ARG GLU GLY THR GLU THR GLY ILE LYS SER SEQRES 14 B 358 LEU GLY VAL ASP VAL ARG VAL CYS ASP ILE GLY ARG ASP SEQRES 15 B 358 ILE ASN GLU VAL ILE SER SER TYR GLU VAL GLU ILE GLY SEQRES 16 B 358 GLY ARG MET TRP PRO ILE ARG PRO ILE SER ASP LEU HIS SEQRES 17 B 358 GLY HIS SER ILE SER GLN PHE ARG ILE HIS GLY GLY ILE SEQRES 18 B 358 SER ILE PRO ALA VAL ASN ASN ARG ASP THR THR ARG ILE SEQRES 19 B 358 LYS GLY ASP SER PHE TYR ALA VAL GLU THR PHE ALA THR SEQRES 20 B 358 THR GLY LYS GLY SER ILE ASP ASP ARG PRO PRO CYS SER SEQRES 21 B 358 HIS PHE VAL LEU ASN THR TYR LYS SER ARG LYS LEU PHE SEQRES 22 B 358 ASN LYS ASP LEU ILE LYS VAL TYR GLU PHE VAL LYS ASP SEQRES 23 B 358 SER LEU GLY THR LEU PRO PHE SER PRO ARG HIS LEU ASP SEQRES 24 B 358 TYR TYR GLY LEU VAL LYS GLY GLY SER LEU LYS SER VAL SEQRES 25 B 358 ASN LEU LEU THR MET MET GLY LEU LEU THR PRO TYR PRO SEQRES 26 B 358 PRO LEU ASN ASP ILE ASP GLY CYS LYS VAL ALA GLN PHE SEQRES 27 B 358 GLU HIS THR VAL TYR LEU SER GLU HIS GLY LYS GLU VAL SEQRES 28 B 358 LEU THR ARG GLY ASP ASP TYR HET FE A 451 1 HET FE A 452 1 HET FUG A 481 24 HET SO4 A 501 5 HET SO4 A 502 5 HET FE B 451 1 HET FE B 452 1 HET FUG B 481 24 HET SO4 B 503 5 HETNAM FE FE (III) ION HETNAM FUG FUMAGILLIN HETNAM SO4 SULFATE ION FORMUL 3 FE 4(FE 3+) FORMUL 5 FUG 2(C26 H36 O7) FORMUL 6 SO4 3(O4 S 2-) FORMUL 12 HOH *227(H2 O) HELIX 1 1 SER A 42 VAL A 66 1 25 HELIX 2 2 THR A 71 LEU A 87 1 17 HELIX 3 3 GLU A 90 ASN A 93 5 4 HELIX 4 4 LYS A 149 ASN A 151 5 3 HELIX 5 5 LEU A 152 LEU A 170 1 19 HELIX 6 6 ARG A 175 SER A 188 1 14 HELIX 7 7 ASN A 274 LEU A 288 1 15 HELIX 8 8 SER A 294 TYR A 301 1 8 HELIX 9 9 SER A 308 MET A 318 1 11 HELIX 10 10 SER B 42 VAL B 66 1 25 HELIX 11 11 THR B 71 LEU B 87 1 17 HELIX 12 12 GLU B 90 ASN B 93 5 4 HELIX 13 13 LYS B 149 ASN B 151 5 3 HELIX 14 14 LEU B 152 LEU B 170 1 19 HELIX 15 15 ARG B 175 SER B 188 1 14 HELIX 16 16 ASN B 274 LEU B 288 1 15 HELIX 17 17 SER B 294 TYR B 301 1 8 HELIX 18 18 SER B 308 MET B 318 1 11 SHEET 1 A 6 GLU A 35 ILE A 36 0 SHEET 2 A 6 LEU A 28 PHE A 29 -1 N LEU A 28 O ILE A 36 SHEET 3 A 6 GLY A 348 VAL A 351 -1 O LYS A 349 N PHE A 29 SHEET 4 A 6 VAL A 335 SER A 345 -1 N TYR A 343 O GLU A 350 SHEET 5 A 6 SER A 238 THR A 247 -1 N TYR A 240 O VAL A 342 SHEET 6 A 6 ARG A 202 PRO A 203 -1 N ARG A 202 O THR A 247 SHEET 1 B 7 GLU A 35 ILE A 36 0 SHEET 2 B 7 LEU A 28 PHE A 29 -1 N LEU A 28 O ILE A 36 SHEET 3 B 7 GLY A 348 VAL A 351 -1 O LYS A 349 N PHE A 29 SHEET 4 B 7 VAL A 335 SER A 345 -1 N TYR A 343 O GLU A 350 SHEET 5 B 7 SER A 238 THR A 247 -1 N TYR A 240 O VAL A 342 SHEET 6 B 7 GLY A 209 ILE A 212 -1 N HIS A 210 O ALA A 241 SHEET 7 B 7 SER A 222 ILE A 223 -1 O ILE A 223 N GLY A 209 SHEET 1 C 3 ILE A 95 MET A 103 0 SHEET 2 C 3 VAL A 126 SER A 135 -1 O ASP A 130 N GLY A 100 SHEET 3 C 3 ARG A 138 ALA A 147 -1 O VAL A 146 N LEU A 127 SHEET 1 D 3 CYS A 106 ALA A 108 0 SHEET 2 D 3 LEU A 327 ASN A 328 -1 O LEU A 327 N ALA A 107 SHEET 3 D 3 ASP A 254 ASP A 255 -1 N ASP A 254 O ASN A 328 SHEET 1 E 2 GLU A 191 GLU A 193 0 SHEET 2 E 2 MET A 198 PRO A 200 -1 O TRP A 199 N VAL A 192 SHEET 1 F 2 PHE A 262 LEU A 264 0 SHEET 2 F 2 LEU A 321 PRO A 323 -1 O THR A 322 N VAL A 263 SHEET 1 G 6 GLU B 35 ILE B 36 0 SHEET 2 G 6 LEU B 28 PHE B 29 -1 N LEU B 28 O ILE B 36 SHEET 3 G 6 GLY B 348 VAL B 351 -1 O LYS B 349 N PHE B 29 SHEET 4 G 6 VAL B 335 SER B 345 -1 N TYR B 343 O GLU B 350 SHEET 5 G 6 SER B 238 THR B 247 -1 N TYR B 240 O VAL B 342 SHEET 6 G 6 ARG B 202 PRO B 203 -1 N ARG B 202 O THR B 247 SHEET 1 H 7 GLU B 35 ILE B 36 0 SHEET 2 H 7 LEU B 28 PHE B 29 -1 N LEU B 28 O ILE B 36 SHEET 3 H 7 GLY B 348 VAL B 351 -1 O LYS B 349 N PHE B 29 SHEET 4 H 7 VAL B 335 SER B 345 -1 N TYR B 343 O GLU B 350 SHEET 5 H 7 SER B 238 THR B 247 -1 N TYR B 240 O VAL B 342 SHEET 6 H 7 GLY B 209 ILE B 212 -1 N HIS B 210 O ALA B 241 SHEET 7 H 7 SER B 222 ILE B 223 -1 O ILE B 223 N GLY B 209 SHEET 1 I 3 ILE B 95 MET B 103 0 SHEET 2 I 3 LEU B 127 SER B 135 -1 O ASP B 130 N GLY B 100 SHEET 3 I 3 ARG B 138 VAL B 146 -1 O MET B 140 N THR B 133 SHEET 1 J 3 CYS B 106 ALA B 108 0 SHEET 2 J 3 LEU B 327 ASN B 328 -1 O LEU B 327 N ALA B 107 SHEET 3 J 3 ASP B 254 ASP B 255 -1 N ASP B 254 O ASN B 328 SHEET 1 K 2 GLU B 191 ILE B 194 0 SHEET 2 K 2 ARG B 197 PRO B 200 -1 O TRP B 199 N VAL B 192 SHEET 1 L 2 PHE B 262 LEU B 264 0 SHEET 2 L 2 LEU B 321 PRO B 323 -1 O THR B 322 N VAL B 263 LINK NE2 HIS A 109 C11 FUG A 481 1555 1555 1.50 LINK NE2 HIS B 109 C11 FUG B 481 1555 1555 1.57 LINK OD1 ASP A 130 FE FE A 452 1555 1555 2.19 LINK OD2 ASP A 130 FE FE A 452 1555 1555 2.38 LINK OD2 ASP A 141 FE FE A 451 1555 1555 2.20 LINK OD1 ASP A 141 FE FE A 452 1555 1555 2.09 LINK NE2 HIS A 210 FE FE A 451 1555 1555 2.21 LINK OE1 GLU A 243 FE FE A 451 1555 1555 2.57 LINK OE2 GLU A 339 FE FE A 451 1555 1555 2.07 LINK OE1 GLU A 339 FE FE A 452 1555 1555 2.05 LINK OD1 ASP B 130 FE FE B 452 1555 1555 2.22 LINK OD2 ASP B 130 FE FE B 452 1555 1555 2.51 LINK OD2 ASP B 141 FE FE B 451 1555 1555 2.28 LINK OD1 ASP B 141 FE FE B 452 1555 1555 2.09 LINK NE2 HIS B 210 FE FE B 451 1555 1555 2.28 LINK OE2 GLU B 243 FE FE B 451 1555 1555 2.47 LINK OE2 GLU B 339 FE FE B 451 1555 1555 2.18 LINK OE1 GLU B 339 FE FE B 452 1555 1555 1.94 CISPEP 1 GLY A 219 GLY A 220 0 1.88 CISPEP 2 PRO A 257 PRO A 258 0 0.30 CISPEP 3 PRO B 257 PRO B 258 0 0.71 SITE 1 AC1 6 ASP A 141 HIS A 210 GLU A 243 GLU A 339 SITE 2 AC1 6 FE A 452 FUG A 481 SITE 1 AC2 5 ASP A 130 ASP A 141 GLU A 243 GLU A 339 SITE 2 AC2 5 FE A 451 SITE 1 AC3 8 HIS A 109 ASP A 206 LEU A 207 HIS A 208 SITE 2 AC3 8 ILE A 217 HIS A 218 TYR A 324 FE A 451 SITE 1 AC4 2 ARG A 77 ARG A 296 SITE 1 AC5 4 LYS A 88 HOH A 605 ARG B 77 ARG B 296 SITE 1 AC6 6 ASP B 141 HIS B 210 GLU B 243 GLU B 339 SITE 2 AC6 6 FE B 452 FUG B 481 SITE 1 AC7 4 ASP B 130 ASP B 141 GLU B 339 FE B 451 SITE 1 AC8 8 HIS B 109 ASP B 206 LEU B 207 HIS B 208 SITE 2 AC8 8 HIS B 218 GLU B 243 TYR B 324 FE B 451 SITE 1 AC9 5 LYS A 305 ARG B 91 PHE B 215 HOH B 598 SITE 2 AC9 5 HOH B 677 CRYST1 62.008 94.238 66.325 90.00 99.43 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 0.016127 0.000000 0.002677 0.00000 SCALE2 0.000000 0.010611 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015284 0.00000