10 20 30 40 50 60 70 80 4I7Y - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE/HYDROLASE INHIBITOR/DNA 01-DEC-12 4I7Y
TITLE CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH A 27-MER TITLE 2 APTAMER BOUND TO EXOSITE II
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: HEAVY CHAIN (UNP RESIDUES 364-622); COMPND 5 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, COMPND 6 ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN HEAVY CHAIN; COMPND 7 EC: 3.4.21.5; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROTHROMBIN; COMPND 10 CHAIN: L; COMPND 11 FRAGMENT: LIGHT CHAIN (UNP RESIDUES 328-363); COMPND 12 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, COMPND 13 ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN LIGHT CHAIN; COMPND 14 EC: 3.4.21.5; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: DNA (27-MER); COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: HD22-27MER
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC DNA; SOURCE 12 ORGANISM_TAXID: 32630
KEYWDS PROTEIN-DNA COMPLEX, SERINE PROTEASE, BLOOD COAGULATION, APTAMER, KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR-DNA COMPLEX, SERINE PROTEASE FOLD, DNA KEYWDS 3 APTAMER, BLOOD, G-QUADRUPLEX, DUPLEX-QUADRUPLEX JUNCTION
EXPDTA X-RAY DIFFRACTION
AUTHOR A.PICA,I.RUSSO KRAUSS,A.MERLINO,L.MAZZARELLA,F.SICA
REVDAT 3 01-JAN-14 4I7Y 1 JRNL REVDAT 2 11-DEC-13 4I7Y 1 JRNL REVDAT 1 16-OCT-13 4I7Y 0
JRNL AUTH I.RUSSO KRAUSS,A.PICA,A.MERLINO,L.MAZZARELLA,F.SICA JRNL TITL DUPLEX-QUADRUPLEX MOTIFS IN A PECULIAR STRUCTURAL JRNL TITL 2 ORGANIZATION COOPERATIVELY CONTRIBUTE TO THROMBIN BINDING OF JRNL TITL 3 A DNA APTAMER. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 2403 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 24311581 JRNL DOI 10.1107/S0907444913022269
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.RUSSO KRAUSS,A.MERLINO,C.GIANCOLA,A.RANDAZZO,L.MAZZARELLA, REMARK 1 AUTH 2 F.SICA REMARK 1 TITL THROMBIN-APTAMER RECOGNITION: A REVEALED AMBIGUITY. REMARK 1 REF NUCLEIC ACIDS RES. V. 39 7858 2011 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 21715374 REMARK 1 DOI 10.1093/NAR/GKR522 REMARK 1 REFERENCE 2 REMARK 1 AUTH I.RUSSO KRAUSS,A.MERLINO,A.RANDAZZO,E.NOVELLINO, REMARK 1 AUTH 2 L.MAZZARELLA,F.SICA REMARK 1 TITL HIGH-RESOLUTION STRUCTURES OF TWO COMPLEXES BETWEEN THROMBIN REMARK 1 TITL 2 AND THROMBIN-BINDING APTAMER SHED LIGHT ON THE ROLE OF REMARK 1 TITL 3 CATIONS IN THE APTAMER INHIBITORY ACTIVITY. REMARK 1 REF NUCLEIC ACIDS RES. V. 40 8119 2012 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 22669903 REMARK 1 DOI 10.1093/NAR/GKS512
REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 16132 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 + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 765 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2244 REMARK 3 NUCLEIC ACID ATOMS : 564 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 98 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 4I7Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-12. REMARK 100 THE RCSB ID CODE IS RCSB076417.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2651 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16132 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL 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) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 3350, 0.2 M SODIUM CITRATE, PH REMARK 280 7.0, 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 40.95200 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, D 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 THR H 146A REMARK 465 TRP H 146B REMARK 465 THR H 146C REMARK 465 ALA H 146D REMARK 465 ASN H 146E REMARK 465 VAL H 146F REMARK 465 GLY H 146G REMARK 465 LYS H 146H REMARK 465 GLU H 247 REMARK 465 THR L -5 REMARK 465 PHE L -4 REMARK 465 GLY L -3 REMARK 465 SER L -2 REMARK 465 GLY L -1 REMARK 465 GLU L 0 REMARK 465 ASP L 15 REMARK 465 GLY L 16 REMARK 465 ARG L 17
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 H 48 -172.31 -170.79 REMARK 500 HIS H 71 -54.59 -124.50 REMARK 500 ASN H 78 19.96 55.32 REMARK 500 ILE H 79 -58.16 -124.19 REMARK 500 ASN H 98 21.59 -151.78 REMARK 500 GLU H 186B 5.14 -68.28 REMARK 500 LYS H 186D 151.87 -45.60 REMARK 500 ASN H 205 38.54 -88.21 REMARK 500 SER H 214 -61.49 -124.23 REMARK 500 ARG H 233 -34.11 -39.39 REMARK 500 PHE L 7 -85.11 -129.93 REMARK 500 SER L 11 50.22 34.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG H 75 TYR H 76 148.59 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 NA H 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 224 O REMARK 620 2 ARG H 221 O 87.8 REMARK 620 3 HOH H 416 O 82.5 95.8 REMARK 620 4 HOH H 453 O 170.8 93.9 88.4 REMARK 620 5 HOH H 411 O 83.6 161.6 99.1 97.1 REMARK 620 6 HOH H 429 O 105.7 76.6 168.4 83.4 90.1 REMARK 620 N 1 2 3 4 5
REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL] REMARK 630 AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 0G6 H 302 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0G6 H 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR MONO-SACCHARIDE NAG L 301 BOUND REMARK 800 TO ASN H 60
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DIH RELATED DB: PDB REMARK 900 RELATED ID: 4DII RELATED DB: PDB REMARK 900 RELATED ID: 3QLP RELATED DB: PDB
DBREF 4I7Y H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 4I7Y L -5 17 UNP P00734 THRB_HUMAN 328 363 DBREF 4I7Y D 1 27 PDB 4I7Y 4I7Y 1 27
SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 L 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 L 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 L 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 D 27 DG DT DC DC DG DT DG DG DT DA DG DG DG SEQRES 2 D 27 DC DA DG DG DT DT DG DG DG DG DT DG DA SEQRES 3 D 27 DC
MODRES 4I7Y ASN H 60G ASN GLYCOSYLATION SITE
HET NAG L 301 14 HET 0G6 H 302 30 HET NA H 303 1
HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM 0G6 D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO) HETNAM 2 0G6 METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L- HETNAM 3 0G6 PROLINAMIDE HETNAM NA SODIUM ION
HETSYN 0G6 PPACK
FORMUL 4 NAG C8 H15 N O6 FORMUL 5 0G6 C21 H34 CL N6 O3 1+ FORMUL 6 NA NA 1+ FORMUL 7 HOH *98(H2 O)
HELIX 1 1 ALA H 55 LEU H 59 1 5 HELIX 2 2 PRO H 60B ASP H 60E 5 4 HELIX 3 3 THR H 60I ASN H 62 5 3 HELIX 4 4 ASP H 125 LEU H 130 1 9 HELIX 5 5 GLU H 164 SER H 171 1 8 HELIX 6 6 LEU H 234 GLY H 246 1 13 HELIX 7 7 PHE L 7 SER L 11 5 5 HELIX 8 8 THR L 14B ILE L 14K 1 10
SHEET 1 A 7 SER H 20 ASP H 21 0 SHEET 2 A 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 A 7 LYS H 135 GLY H 140 -1 N GLY H 136 O LEU H 160 SHEET 4 A 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 A 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 A 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215 SHEET 7 A 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 B 7 LYS H 81 SER H 83 0 SHEET 2 B 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 3 B 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 4 B 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 SHEET 5 B 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 6 B 7 ALA H 104 LEU H 108 -1 O MET H 106 N VAL H 52 SHEET 7 B 7 LEU H 85 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 1 C 2 LEU H 60 TYR H 60A 0 SHEET 2 C 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A
SSBOND 1 CYS H 42 CYS H 58 1555 1555 2.07 SSBOND 2 CYS H 122 CYS L 1 1555 1555 2.04 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.05
LINK ND2 ASN H 60G C1 NAG L 301 1555 1555 1.46 LINK O LYS H 224 NA NA H 303 1555 1555 2.27 LINK O ARG H 221 NA NA H 303 1555 1555 2.43 LINK OG SER H 195 C2 0G6 H 302 1555 1555 1.42 LINK NE2 HIS H 57 C3 0G6 H 302 1555 1555 1.50 LINK NA NA H 303 O HOH H 416 1555 1555 2.20 LINK NA NA H 303 O HOH H 453 1555 1555 2.26 LINK NA NA H 303 O HOH H 411 1555 1555 2.35 LINK NA NA H 303 O HOH H 429 1555 1555 2.50
CISPEP 1 SER H 36A PRO H 37 0 -5.44
SITE 1 AC1 15 HIS H 57 TYR H 60A LEU H 99 ASP H 189 SITE 2 AC1 15 ALA H 190 GLY H 193 ASP H 194 SER H 195 SITE 3 AC1 15 SER H 214 TRP H 215 GLY H 216 GLY H 219 SITE 4 AC1 15 GLY H 226 HOH H 412 HOH H 438 SITE 1 AC2 6 ARG H 221 LYS H 224 HOH H 411 HOH H 416 SITE 2 AC2 6 HOH H 429 HOH H 453 SITE 1 AC3 1 ASN H 60G
CRYST1 48.144 81.904 53.720 90.00 99.66 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 0.020771 0.000000 0.003536 0.00000
SCALE2 0.000000 0.012209 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018883 0.00000