1AK0 - Header Asymmetric Unit

HEADER ENDONUCLEASE 28-MAY-97 1AK0

TITLE P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG

COMPND MOL_ID: 1; COMPND 2 MOLECULE: P1 NUCLEASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.30.1

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PENICILLIUM CITRINUM; SOURCE 3 ORGANISM_TAXID: 5077

KEYWDS ENDONUCLEASE, P1 NUCLEASE, REACTION MECHANISM, THIOPHOSPHORYLATED KEYWDS 2 OLIGONUCLEOTIDES, GLYCOSYLATED PROTEIN

EXPDTA X-RAY DIFFRACTION

AUTHOR C.ROMIER,D.SUCK

REVDAT 3 13-JUL-11 1AK0 1 VERSN REVDAT 2 24-FEB-09 1AK0 1 VERSN REVDAT 1 03-DEC-97 1AK0 0

JRNL AUTH C.ROMIER,R.DOMINGUEZ,A.LAHM,O.DAHL,D.SUCK JRNL TITL RECOGNITION OF SINGLE-STRANDED DNA BY NUCLEASE P1: HIGH JRNL TITL 2 RESOLUTION CRYSTAL STRUCTURES OF COMPLEXES WITH SUBSTRATE JRNL TITL 3 ANALOGS. JRNL REF PROTEINS V. 32 414 1998 JRNL REFN ISSN 0887-3585 JRNL PMID 9726413 JRNL DOI 10.1002/(SICI)1097-0134(19980901)32:4<414::AID-PROT JRNL DOI 2 2>3.3.CO;2-5

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.VOLBEDA,A.LAHM,F.SAKIYAMA,D.SUCK REMARK 1 TITL CRYSTAL STRUCTURE OF PENICILLIUM CITRINUM P1 NUCLEASE AT 2.8 REMARK 1 TITL 2 A RESOLUTION REMARK 1 REF EMBO J. V. 10 1607 1991 REMARK 1 REFN ISSN 0261-4189

REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.1 REMARK 3 NUMBER OF REFLECTIONS : 27019 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL 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 : 2021 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 138 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.70 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.500 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.500 ; NULL 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM3.CHO REMARK 3 PARAMETER FILE 3 : PARNAH1E.DNA REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH3.CHO REMARK 3 TOPOLOGY FILE 3 : TOPNAH1E.DNA REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1AK0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JAN-94 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27854 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24700 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000 12 - 20% 25 MM NA ACETATE PH REMARK 280 5.3

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 20.99000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.06500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.02000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.06500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.99000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.02000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL

REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.

REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 265 REMARK 465 SER A 266 REMARK 465 GLU A 267 REMARK 465 ILE A 268 REMARK 465 ALA A 269 REMARK 465 LYS A 270

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 O7 NAG A 287 O HOH A 552 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 GLU A 105 CB - CA - C ANGL. DEV. = 13.2 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 ASP A 66 -158.88 -110.16 REMARK 500 TYR A 130 125.45 -37.70 REMARK 500 ASP A 146 -169.64 -112.59 REMARK 500 THR A 154 -58.80 -122.14 REMARK 500 SER A 182 58.71 -149.34 REMARK 500 GLU A 200 55.30 -145.62 REMARK 500 GLN A 229 36.12 -99.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 GLU A 105 17.5 L L OUTSIDE RANGE REMARK 500 THR A 230 24.7 L L OUTSIDE RANGE 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 526 DISTANCE = 5.67 ANGSTROMS

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 ADS A 292

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 271 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 60 ND1 REMARK 620 2 HIS A 116 NE2 101.4 REMARK 620 3 ASP A 120 OD2 103.5 98.0 REMARK 620 4 ASP A 45 OD1 80.7 75.0 172.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 272 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 126 NE2 REMARK 620 2 HIS A 149 NE2 95.3 REMARK 620 3 ASP A 153 OD2 143.9 96.0 REMARK 620 4 THS A 295 O3' 111.2 100.2 100.3 REMARK 620 5 ASP A 153 OD1 93.9 92.2 51.5 150.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 273 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 1 O REMARK 620 2 HIS A 6 NE2 99.8 REMARK 620 3 ASP A 120 OD1 166.3 87.5 REMARK 620 4 TRP A 1 N 72.5 113.2 94.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 274 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 15 NE2 REMARK 620 2 GLU A 181 CD 104.9 REMARK 620 3 GLU A 181 OE2 87.5 30.9 REMARK 620 4 HOH A 539 O 96.5 131.5 161.5 REMARK 620 5 GLU A 181 OE1 104.8 29.5 58.3 103.2 REMARK 620 6 HIS A 223 ND1 106.9 104.4 85.7 110.2 130.2 REMARK 620 N 1 2 3 4 5

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 281 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 285 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 271 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 272 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 273 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 274 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADS A 292 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THS A 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THS A 294 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THS A 295

DBREF 1AK0 A 1 270 UNP P24289 NUP1_PENCI 1 270

SEQRES 1 A 270 TRP GLY ALA LEU GLY HIS ALA THR VAL ALA TYR VAL ALA SEQRES 2 A 270 GLN HIS TYR VAL SER PRO GLU ALA ALA SER TRP ALA GLN SEQRES 3 A 270 GLY ILE LEU GLY SER SER SER SER SER TYR LEU ALA SER SEQRES 4 A 270 ILE ALA SER TRP ALA ASP GLU TYR ARG LEU THR SER ALA SEQRES 5 A 270 GLY LYS TRP SER ALA SER LEU HIS PHE ILE ASP ALA GLU SEQRES 6 A 270 ASP ASN PRO PRO THR ASN CYS ASN VAL ASP TYR GLU ARG SEQRES 7 A 270 ASP CYS GLY SER SER GLY CYS SER ILE SER ALA ILE ALA SEQRES 8 A 270 ASN TYR THR GLN ARG VAL SER ASP SER SER LEU SER SER SEQRES 9 A 270 GLU ASN HIS ALA GLU ALA LEU ARG PHE LEU VAL HIS PHE SEQRES 10 A 270 ILE GLY ASP MET THR GLN PRO LEU HIS ASP GLU ALA TYR SEQRES 11 A 270 ALA VAL GLY GLY ASN LYS ILE ASN VAL THR PHE ASP GLY SEQRES 12 A 270 TYR HIS ASP ASN LEU HIS SER ASP TRP ASP THR TYR MET SEQRES 13 A 270 PRO GLN LYS LEU ILE GLY GLY HIS ALA LEU SER ASP ALA SEQRES 14 A 270 GLU SER TRP ALA LYS THR LEU VAL GLN ASN ILE GLU SER SEQRES 15 A 270 GLY ASN TYR THR ALA GLN ALA ILE GLY TRP ILE LYS GLY SEQRES 16 A 270 ASP ASN ILE SER GLU PRO ILE THR THR ALA THR ARG TRP SEQRES 17 A 270 ALA SER ASP ALA ASN ALA LEU VAL CYS THR VAL VAL MET SEQRES 18 A 270 PRO HIS GLY ALA ALA ALA LEU GLN THR GLY ASP LEU TYR SEQRES 19 A 270 PRO THR TYR TYR ASP SER VAL ILE ASP THR ILE GLU LEU SEQRES 20 A 270 GLN ILE ALA LYS GLY GLY TYR ARG LEU ALA ASN TRP ILE SEQRES 21 A 270 ASN GLU ILE HIS GLY SER GLU ILE ALA LYS

MODRES 1AK0 ASN A 92 ASN GLYCOSYLATION SITE MODRES 1AK0 ASN A 197 ASN GLYCOSYLATION SITE MODRES 1AK0 ASN A 138 ASN GLYCOSYLATION SITE

HET NAG A 281 14 HET NAG A 282 14 HET NAG A 285 14 HET NAG A 287 14 HET ZN A 271 1 HET ZN A 272 1 HET ZN A 273 1 HET ZN A 274 1 HET ADS A 292 18 HET THS A 293 20 HET THS A 294 20 HET THS A 295 20

HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM ZN ZINC ION HETNAM ADS ADENOSINE-5'-(DITHIO)PHOSPHATE HETNAM THS THYMIDINE-5'-(DITHIO)PHOSPHATE

FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 5 ZN 4(ZN 2+) FORMUL 9 ADS C10 H14 N5 O5 P S2 FORMUL 9 THS 3(C10 H15 N2 O6 P S2) FORMUL 10 HOH *154(H2 O)

HELIX 1 1 ALA A 3 TYR A 16 1 14 HELIX 2 2 PRO A 19 LEU A 29 1 11 HELIX 3 3 ALA A 38 ILE A 40 5 3 HELIX 4 4 TRP A 43 LEU A 49 1 7 HELIX 5 5 LYS A 54 HIS A 60 5 7 HELIX 6 6 TYR A 76 ASP A 79 1 4 HELIX 7 7 SER A 86 VAL A 97 1 12 HELIX 8 8 SER A 104 THR A 122 1 19 HELIX 9 9 PRO A 124 ASP A 127 5 4 HELIX 10 10 TYR A 130 GLY A 133 1 4 HELIX 11 11 LEU A 148 ASP A 153 1 6 HELIX 12 12 TYR A 155 ILE A 161 1 7 HELIX 13 13 LEU A 166 SER A 182 1 17 HELIX 14 14 THR A 186 TRP A 192 1 7 HELIX 15 15 ILE A 198 THR A 218 5 21 HELIX 16 16 ALA A 226 LEU A 228 5 3 HELIX 17 17 THR A 236 GLU A 262 1 27

SHEET 1 A 2 ASN A 138 PHE A 141 0 SHEET 2 A 2 TYR A 144 ASN A 147 -1 N ASP A 146 O VAL A 139

SSBOND 1 CYS A 72 CYS A 217 1555 1555 2.03 SSBOND 2 CYS A 80 CYS A 85 1555 1555 2.05

LINK ZN ZN A 271 ND1 HIS A 60 1555 1555 2.31 LINK ZN ZN A 271 NE2 HIS A 116 1555 1555 2.29 LINK ZN ZN A 271 OD2 ASP A 120 1555 1555 2.01 LINK ZN ZN A 272 NE2 HIS A 126 1555 1555 2.32 LINK ZN ZN A 272 NE2 HIS A 149 1555 1555 2.31 LINK ZN ZN A 272 OD2 ASP A 153 1555 1555 1.97 LINK ZN ZN A 272 O3' THS A 295 1555 1555 2.02 LINK ZN ZN A 273 O TRP A 1 1555 1555 2.00 LINK ZN ZN A 273 NE2 HIS A 6 1555 1555 2.27 LINK ZN ZN A 273 OD1 ASP A 120 1555 1555 1.98 LINK ZN ZN A 274 NE2 HIS A 15 1555 1555 2.22 LINK ZN ZN A 274 CD GLU A 181 1555 1555 2.36 LINK ZN ZN A 274 OE2 GLU A 181 1555 1555 1.81 LINK C1 NAG A 281 ND2 ASN A 92 1555 1555 1.46 LINK O4 NAG A 281 C1 NAG A 282 1555 1555 1.39 LINK C1 NAG A 285 ND2 ASN A 197 1555 1555 1.47 LINK C1 NAG A 287 ND2 ASN A 138 1555 1555 1.45 LINK O3' ADS A 292 P THS A 293 1555 1555 1.64 LINK O3' THS A 293 P THS A 294 1555 1555 1.67 LINK O3' THS A 294 P THS A 295 1555 1555 1.64 LINK ZN ZN A 271 OD1 ASP A 45 1555 1555 2.77 LINK ZN ZN A 272 OD1 ASP A 153 1555 1555 2.78 LINK ZN ZN A 273 N TRP A 1 1555 1555 2.53 LINK ZN ZN A 274 O HOH A 539 1555 1555 2.02 LINK ZN ZN A 274 OE1 GLU A 181 1555 1555 2.49 LINK ZN ZN A 274 ND1 HIS A 223 1555 3655 2.22

CISPEP 1 PRO A 68 PRO A 69 0 0.35 CISPEP 2 TYR A 234 PRO A 235 0 -4.87

SITE 1 AC1 6 ASN A 92 TYR A 93 ARG A 96 GLU A 109 SITE 2 AC1 6 NAG A 282 HOH A 551 SITE 1 AC2 3 TRP A 55 NAG A 281 HOH A 516 SITE 1 AC3 3 ASN A 197 SER A 199 HOH A 540 SITE 1 AC4 2 ASN A 138 HOH A 552 SITE 1 AC5 5 ASP A 45 HIS A 60 HIS A 116 ASP A 120 SITE 2 AC5 5 ZN A 273 SITE 1 AC6 4 HIS A 126 HIS A 149 ASP A 153 THS A 295 SITE 1 AC7 4 TRP A 1 HIS A 6 ASP A 120 ZN A 271 SITE 1 AC8 4 HIS A 15 GLU A 181 HIS A 223 HOH A 539 SITE 1 AC9 8 ASN A 71 ASN A 73 PHE A 141 TYR A 144 SITE 2 AC9 8 ASP A 146 TYR A 155 THS A 293 HOH A 441 SITE 1 BC1 9 ASP A 66 ASN A 67 ASN A 73 ASP A 75 SITE 2 BC1 9 ARG A 78 HIS A 164 ADS A 292 THS A 294 SITE 3 BC1 9 HOH A 519 SITE 1 BC2 4 GLU A 77 LYS A 136 THS A 293 THS A 295 SITE 1 BC3 11 PHE A 61 ASP A 63 LEU A 125 HIS A 126 SITE 2 BC3 11 ASN A 135 HIS A 149 ASP A 153 ZN A 272 SITE 3 BC3 11 THS A 294 HOH A 428 HOH A 429

CRYST1 41.980 74.040 102.130 90.00 90.00 90.00 P 21 21 21 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 0.023821 0.000000 0.000000 0.00000

SCALE2 0.000000 0.013506 0.000000 0.00000

SCALE3 0.000000 0.000000 0.009791 0.00000