HEADER METAL BINDING PROTEIN 23-AUG-11 3VH2 TITLE CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE ATG7 (1-613) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME ATG7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-613; COMPND 5 SYNONYM: ATG12-ACTIVATING ENZYME E1 ATG7, AUTOPHAGY-RELATED PROTEIN COMPND 6 7, CYTOPLASM TO VACUOLE TARGETING PROTEIN 2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: S288C; SOURCE 6 GENE: ATG7, APG7, CVT2, YHR171W; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEX6P KEYWDS AUTOPHAGY, E1, ZINC BINDING, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.N.NODA,K.SATOO,F.INAGAKI REVDAT 4 08-NOV-23 3VH2 1 REMARK SEQADV LINK REVDAT 3 28-MAR-12 3VH2 1 JRNL REVDAT 2 16-NOV-11 3VH2 1 JRNL REVDAT 1 21-SEP-11 3VH2 0 JRNL AUTH N.N.NODA,K.SATOO,Y.FUJIOKA,H.KUMETA,K.OGURA,H.NAKATOGAWA, JRNL AUTH 2 Y.OHSUMI,F.INAGAKI JRNL TITL STRUCTURAL BASIS OF ATG8 ACTIVATION BY A HOMODIMERIC E1, JRNL TITL 2 ATG7. JRNL REF MOL.CELL V. 44 462 2011 JRNL REFN ISSN 1097-2765 JRNL PMID 22055191 JRNL DOI 10.1016/J.MOLCEL.2011.08.035 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 33890.550 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 17861 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 SET) : 0.216 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1766 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.51 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2445 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 264 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4584 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.64000 REMARK 3 B22 (A**2) : 7.64000 REMARK 3 B33 (A**2) : -15.28000 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) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.57 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.64 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.340 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.620 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.660 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 25.06 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3VH2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000095035. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18578 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3VH1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9-13% ETHYLENE GLYCOL, 150MM NACL, REMARK 280 20MM TRIS, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.08300 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 176.16600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 176.16600 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 88.08300 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 176.16600 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 GLY A -2 REMARK 465 PRO A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 VAL A 32 REMARK 465 LEU A 33 REMARK 465 LYS A 34 REMARK 465 LEU A 35 REMARK 465 ASP A 36 REMARK 465 SER A 37 REMARK 465 PRO A 259 REMARK 465 GLN A 260 REMARK 465 SER A 261 REMARK 465 SER A 262 REMARK 465 SER A 263 REMARK 465 SER A 264 REMARK 465 ASN A 265 REMARK 465 ASN A 474 REMARK 465 ARG A 475 REMARK 465 ASP A 476 REMARK 465 GLU A 477 REMARK 465 GLN A 478 REMARK 465 SER A 479 REMARK 465 SER A 480 REMARK 465 LYS A 481 REMARK 465 VAL A 606 REMARK 465 ILE A 607 REMARK 465 LYS A 608 REMARK 465 GLN A 609 REMARK 465 GLU A 610 REMARK 465 VAL A 611 REMARK 465 GLU A 612 REMARK 465 ARG A 613 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 LYS A 53 CG CD CE NZ REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 HIS A 70 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 132 CG CD CE NZ REMARK 470 LYS A 170 CG CD CE NZ REMARK 470 ARG A 198 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 258 CG OD1 OD2 REMARK 470 LYS A 269 CG CD CE NZ REMARK 470 LYS A 409 CG CD CE NZ REMARK 470 GLN A 482 CG CD OE1 NE2 REMARK 470 ASP A 490 CG OD1 OD2 REMARK 470 VAL A 491 CG1 CG2 REMARK 470 LYS A 533 CG CD CE NZ REMARK 470 LYS A 589 CG CD CE NZ REMARK 470 LYS A 590 CG CD CE NZ REMARK 470 SER A 605 OG 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 ARG A 5 172.02 178.67 REMARK 500 ASN A 72 89.11 -150.53 REMARK 500 PRO A 143 106.75 -53.92 REMARK 500 VAL A 152 -167.96 -109.14 REMARK 500 SER A 160 156.74 -36.87 REMARK 500 MET A 211 117.45 -37.76 REMARK 500 ASN A 213 19.56 50.65 REMARK 500 PHE A 236 -168.18 -166.45 REMARK 500 ASN A 244 -134.03 -170.05 REMARK 500 SER A 256 102.96 -176.04 REMARK 500 LEU A 314 67.17 -158.31 REMARK 500 ALA A 368 26.09 -56.48 REMARK 500 LEU A 369 17.63 -142.50 REMARK 500 ASP A 374 34.52 -93.44 REMARK 500 ASP A 395 79.02 -103.71 REMARK 500 LYS A 409 111.35 -25.45 REMARK 500 ASN A 412 73.11 53.40 REMARK 500 GLU A 414 -72.15 -58.04 REMARK 500 GLU A 429 2.36 -57.70 REMARK 500 TRP A 444 -79.92 -56.87 REMARK 500 THR A 495 26.81 -73.61 REMARK 500 ARG A 501 2.50 -69.85 REMARK 500 GLN A 505 52.23 -106.21 REMARK 500 MET A 506 17.66 58.13 REMARK 500 SER A 537 156.40 162.56 REMARK 500 GLU A 538 57.07 -107.87 REMARK 500 ILE A 545 58.17 -148.06 REMARK 500 PRO A 546 165.58 -43.84 REMARK 500 PHE A 556 76.11 55.07 REMARK 500 ALA A 571 -46.51 -130.41 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 ZN A 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 193 OD1 REMARK 620 2 CYS A 195 SG 92.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 485 SG REMARK 620 2 CYS A 488 SG 112.3 REMARK 620 3 CYS A 569 SG 97.0 140.9 REMARK 620 4 CYS A 572 SG 94.4 103.9 98.8 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 ZN A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VH1 RELATED DB: PDB REMARK 900 THE SAME PROTEIN AS A FREE FORM. REMARK 900 RELATED ID: 3VH3 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEX WITHOUT MGATP. REMARK 900 RELATED ID: 3VH4 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEX WITH MGATP. DBREF 3VH2 A 1 613 UNP P38862 ATG7_YEAST 1 613 SEQADV 3VH2 GLY A -2 UNP P38862 EXPRESSION TAG SEQADV 3VH2 PRO A -1 UNP P38862 EXPRESSION TAG SEQADV 3VH2 HIS A 0 UNP P38862 EXPRESSION TAG SEQRES 1 A 616 GLY PRO HIS MET SER SER GLU ARG VAL LEU SER TYR ALA SEQRES 2 A 616 PRO ALA PHE LYS SER PHE LEU ASP THR SER PHE PHE GLN SEQRES 3 A 616 GLU LEU SER ARG LEU LYS LEU ASP VAL LEU LYS LEU ASP SEQRES 4 A 616 SER THR CYS GLN PRO LEU THR VAL ASN LEU ASP LEU HIS SEQRES 5 A 616 ASN ILE PRO LYS SER ALA ASP GLN VAL PRO LEU PHE LEU SEQRES 6 A 616 THR ASN ARG SER PHE GLU LYS HIS ASN ASN LYS ARG THR SEQRES 7 A 616 ASN GLU VAL PRO LEU GLN GLY SER ILE PHE ASN PHE ASN SEQRES 8 A 616 VAL LEU ASP GLU PHE LYS ASN LEU ASP LYS GLN LEU PHE SEQRES 9 A 616 LEU HIS GLN ARG ALA LEU GLU CYS TRP GLU ASP GLY ILE SEQRES 10 A 616 LYS ASP ILE ASN LYS CYS VAL SER PHE VAL ILE ILE SER SEQRES 11 A 616 PHE ALA ASP LEU LYS LYS TYR ARG PHE TYR TYR TRP LEU SEQRES 12 A 616 GLY VAL PRO CYS PHE GLN ARG PRO SER SER THR VAL LEU SEQRES 13 A 616 HIS VAL ARG PRO GLU PRO SER LEU LYS GLY LEU PHE SER SEQRES 14 A 616 LYS CYS GLN LYS TRP PHE ASP VAL ASN TYR SER LYS TRP SEQRES 15 A 616 VAL CYS ILE LEU ASP ALA ASP ASP GLU ILE VAL ASN TYR SEQRES 16 A 616 ASP LYS CYS ILE ILE ARG LYS THR LYS VAL LEU ALA ILE SEQRES 17 A 616 ARG ASP THR SER THR MET GLU ASN VAL PRO SER ALA LEU SEQRES 18 A 616 THR LYS ASN PHE LEU SER VAL LEU GLN TYR ASP VAL PRO SEQRES 19 A 616 ASP LEU ILE ASP PHE LYS LEU LEU ILE ILE ARG GLN ASN SEQRES 20 A 616 GLU GLY SER PHE ALA LEU ASN ALA THR PHE ALA SER ILE SEQRES 21 A 616 ASP PRO GLN SER SER SER SER ASN PRO ASP MET LYS VAL SEQRES 22 A 616 SER GLY TRP GLU ARG ASN VAL GLN GLY LYS LEU ALA PRO SEQRES 23 A 616 ARG VAL VAL ASP LEU SER SER LEU LEU ASP PRO LEU LYS SEQRES 24 A 616 ILE ALA ASP GLN SER VAL ASP LEU ASN LEU LYS LEU MET SEQRES 25 A 616 LYS TRP ARG ILE LEU PRO ASP LEU ASN LEU ASP ILE ILE SEQRES 26 A 616 LYS ASN THR LYS VAL LEU LEU LEU GLY ALA GLY THR LEU SEQRES 27 A 616 GLY CYS TYR VAL SER ARG ALA LEU ILE ALA TRP GLY VAL SEQRES 28 A 616 ARG LYS ILE THR PHE VAL ASP ASN GLY THR VAL SER TYR SEQRES 29 A 616 SER ASN PRO VAL ARG GLN ALA LEU TYR ASN PHE GLU ASP SEQRES 30 A 616 CYS GLY LYS PRO LYS ALA GLU LEU ALA ALA ALA SER LEU SEQRES 31 A 616 LYS ARG ILE PHE PRO LEU MET ASP ALA THR GLY VAL LYS SEQRES 32 A 616 LEU SER ILE PRO MET ILE GLY HIS LYS LEU VAL ASN GLU SEQRES 33 A 616 GLU ALA GLN HIS LYS ASP PHE ASP ARG LEU ARG ALA LEU SEQRES 34 A 616 ILE LYS GLU HIS ASP ILE ILE PHE LEU LEU VAL ASP SER SEQRES 35 A 616 ARG GLU SER ARG TRP LEU PRO SER LEU LEU SER ASN ILE SEQRES 36 A 616 GLU ASN LYS THR VAL ILE ASN ALA ALA LEU GLY PHE ASP SEQRES 37 A 616 SER TYR LEU VAL MET ARG HIS GLY ASN ARG ASP GLU GLN SEQRES 38 A 616 SER SER LYS GLN LEU GLY CYS TYR PHE CYS HIS ASP VAL SEQRES 39 A 616 VAL ALA PRO THR ASP SER LEU THR ASP ARG THR LEU ASP SEQRES 40 A 616 GLN MET CYS THR VAL THR ARG PRO GLY VAL ALA MET MET SEQRES 41 A 616 ALA SER SER LEU ALA VAL GLU LEU MET THR SER LEU LEU SEQRES 42 A 616 GLN THR LYS TYR SER GLY SER GLU THR THR VAL LEU GLY SEQRES 43 A 616 ASP ILE PRO HIS GLN ILE ARG GLY PHE LEU HIS ASN PHE SEQRES 44 A 616 SER ILE LEU LYS LEU GLU THR PRO ALA TYR GLU HIS CYS SEQRES 45 A 616 PRO ALA CYS SER PRO LYS VAL ILE GLU ALA PHE THR ASP SEQRES 46 A 616 LEU GLY TRP GLU PHE VAL LYS LYS ALA LEU GLU HIS PRO SEQRES 47 A 616 LEU TYR LEU GLU GLU ILE SER GLY LEU SER VAL ILE LYS SEQRES 48 A 616 GLN GLU VAL GLU ARG HET ZN A 701 1 HET ZN A 702 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 ASP A 18 LEU A 30 1 13 HELIX 2 2 VAL A 89 ASN A 95 1 7 HELIX 3 3 ASP A 97 ILE A 114 1 18 HELIX 4 4 ASP A 116 CYS A 120 5 5 HELIX 5 5 LEU A 161 ASN A 175 1 15 HELIX 6 6 ASP A 193 LYS A 201 1 9 HELIX 7 7 LEU A 218 VAL A 230 1 13 HELIX 8 8 LEU A 288 ASP A 293 1 6 HELIX 9 9 ASP A 293 LEU A 314 1 22 HELIX 10 10 ASN A 318 ASN A 324 1 7 HELIX 11 11 GLY A 333 ALA A 345 1 13 HELIX 12 12 ASN A 371 CYS A 375 5 5 HELIX 13 13 PRO A 378 PHE A 391 1 14 HELIX 14 14 ASN A 412 HIS A 430 1 19 HELIX 15 15 SER A 439 SER A 442 5 4 HELIX 16 16 ARG A 443 GLU A 453 1 11 HELIX 17 17 PRO A 512 LEU A 529 1 18 HELIX 18 18 SER A 573 LEU A 583 1 11 HELIX 19 19 GLY A 584 HIS A 594 1 11 HELIX 20 20 HIS A 594 GLY A 603 1 10 SHEET 1 A 7 ARG A 5 VAL A 6 0 SHEET 2 A 7 LEU A 153 GLU A 158 -1 O VAL A 155 N ARG A 5 SHEET 3 A 7 PHE A 248 PHE A 254 -1 O ASN A 251 N ARG A 156 SHEET 4 A 7 ASP A 235 ILE A 241 -1 N LEU A 238 O LEU A 250 SHEET 5 A 7 VAL A 202 ARG A 206 1 N ILE A 205 O LEU A 239 SHEET 6 A 7 VAL A 180 LEU A 183 -1 N CYS A 181 O ALA A 204 SHEET 7 A 7 ILE A 189 ASN A 191 -1 O VAL A 190 N ILE A 182 SHEET 1 B 2 LYS A 14 LEU A 17 0 SHEET 2 B 2 PRO A 59 LEU A 62 1 O LEU A 60 N LYS A 14 SHEET 1 C 5 CYS A 39 LEU A 46 0 SHEET 2 C 5 VAL A 78 PHE A 87 -1 O GLY A 82 N LEU A 42 SHEET 3 C 5 PHE A 123 ASP A 130 1 O ILE A 125 N PHE A 85 SHEET 4 C 5 ARG A 135 GLN A 146 -1 O GLY A 141 N VAL A 124 SHEET 5 C 5 LYS A 269 TRP A 273 -1 O GLY A 272 N VAL A 142 SHEET 1 D 5 CYS A 39 LEU A 46 0 SHEET 2 D 5 VAL A 78 PHE A 87 -1 O GLY A 82 N LEU A 42 SHEET 3 D 5 PHE A 123 ASP A 130 1 O ILE A 125 N PHE A 85 SHEET 4 D 5 ARG A 135 GLN A 146 -1 O GLY A 141 N VAL A 124 SHEET 5 D 5 ARG A 284 ASP A 287 -1 O ARG A 284 N TYR A 138 SHEET 1 E 8 ASP A 395 VAL A 399 0 SHEET 2 E 8 LYS A 350 VAL A 354 1 N PHE A 353 O THR A 397 SHEET 3 E 8 LYS A 326 LEU A 330 1 N LEU A 329 O THR A 352 SHEET 4 E 8 ILE A 432 LEU A 435 1 O PHE A 434 N LEU A 328 SHEET 5 E 8 THR A 456 LEU A 462 1 O THR A 456 N ILE A 433 SHEET 6 E 8 SER A 466 HIS A 472 -1 O MET A 470 N ASN A 459 SHEET 7 E 8 GLN A 548 PHE A 552 -1 O ILE A 549 N VAL A 469 SHEET 8 E 8 SER A 557 LEU A 561 -1 O LEU A 559 N ARG A 550 SHEET 1 F 2 THR A 539 THR A 540 0 SHEET 2 F 2 GLY A 543 ASP A 544 -1 O GLY A 543 N THR A 540 LINK OD1 ASP A 193 ZN ZN A 702 1555 1555 2.30 LINK SG CYS A 195 ZN ZN A 702 1555 1555 2.45 LINK SG CYS A 485 ZN ZN A 701 1555 1555 2.59 LINK SG CYS A 488 ZN ZN A 701 1555 1555 2.19 LINK SG CYS A 569 ZN ZN A 701 1555 1555 2.40 LINK SG CYS A 572 ZN ZN A 701 1555 1555 2.23 CISPEP 1 ARG A 147 PRO A 148 0 0.34 SITE 1 AC1 4 CYS A 485 CYS A 488 CYS A 569 CYS A 572 SITE 1 AC2 3 ASP A 193 CYS A 195 HIS A 408 CRYST1 88.028 88.028 264.249 90.00 90.00 120.00 P 31 2 1 6 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 0.011360 0.006559 0.000000 0.00000 SCALE2 0.000000 0.013117 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003784 0.00000