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- PDB-1ucy: THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ucy | |||||||||
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Title | THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). THREE COMPLEXES, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN | |||||||||
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![]() | COMPLEX (SERINE PROTEASE/COAGULATION) / COMPLEX (SERINE PROTEASE-COAGULATION) / SERINE / PROTEASE / THROMBIN / COMPLEX (SERINE PROTEASE-COAGULATION) complex | |||||||||
Function / homology | ![]() fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / blood coagulation / collagen-containing extracellular matrix / adaptive immune response / serine-type endopeptidase activity ...fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / blood coagulation / collagen-containing extracellular matrix / adaptive immune response / serine-type endopeptidase activity / innate immune response / calcium ion binding / proteolysis / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Martin, P. / Edwards, B. | |||||||||
![]() | ![]() Title: Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen A alpha: geometry of the catalytic triad and interactions of the P1', P2', and P3' substrate residues. Authors: Martin, P.D. / Malkowski, M.G. / DiMaio, J. / Konishi, Y. / Ni, F. / Edwards, B.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.4 KB | Display | ![]() |
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PDB format | ![]() | 170.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein/peptide , 2 types, 6 molecules LJMFGI
#1: Protein/peptide | Mass: 5735.240 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. ...Details: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. 226, 1085). THE N-TERMINUS OF THE FIBRINOPEPTIDE IS ACETYLATED. FIBRINOPEPTIDE SEQUENCE NUMBERS ARE ACE 6 TO ARG 19. A NEW RESIDUE, OPR, HAS BEEN DEFINED FOR THE ARG/GLY COMBINATION IN WHICH THE AMIDE NITROGEN HAS BEEN REPLACED WITH A CH2, MAKING THE NORMAL AMIDE BOND BETWEEN THESE TWO RESIDUES A KETONE BOND. THE FIBRINOPEPTIDE NUMBERING IS CONSEQUENTLY INCREMENTED BY 1 AFTER THIS RESIDUE IN KEEPING WITH THE FIBRINOGEN NUMBERING SCHEME. THERE ARE ALTERNATE CONFORMATIONS FOR RESIDUES PRO 18 AND ARG 19 IN FIBRINOPEPTIDE III. Source: (natural) ![]() ![]() #4: Protein/peptide | Mass: 1356.508 Da / Num. of mol.: 3 / Fragment: RESIDUES 7 - 19 Source method: isolated from a genetically manipulated source Details: THREE COMPLEXES ARE PRESENTED, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN References: UniProt: P12803, UniProt: P68108*PLUS |
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-Protein , 3 types, 4 molecules HEKN
#2: Protein | Mass: 17525.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. ...Details: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. 226, 1085). THE N-TERMINUS OF THE FIBRINOPEPTIDE IS ACETYLATED. FIBRINOPEPTIDE SEQUENCE NUMBERS ARE ACE 6 TO ARG 19. A NEW RESIDUE, OPR, HAS BEEN DEFINED FOR THE ARG/GLY COMBINATION IN WHICH THE AMIDE NITROGEN HAS BEEN REPLACED WITH A CH2, MAKING THE NORMAL AMIDE BOND BETWEEN THESE TWO RESIDUES A KETONE BOND. THE FIBRINOPEPTIDE NUMBERING IS CONSEQUENTLY INCREMENTED BY 1 AFTER THIS RESIDUE IN KEEPING WITH THE FIBRINOGEN NUMBERING SCHEME. THERE ARE ALTERNATE CONFORMATIONS FOR RESIDUES PRO 18 AND ARG 19 IN FIBRINOPEPTIDE III. Source: (natural) ![]() ![]() |
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#3: Protein | Mass: 12265.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. ...Details: CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. 226, 1085). THE N-TERMINUS OF THE FIBRINOPEPTIDE IS ACETYLATED. FIBRINOPEPTIDE SEQUENCE NUMBERS ARE ACE 6 TO ARG 19. A NEW RESIDUE, OPR, HAS BEEN DEFINED FOR THE ARG/GLY COMBINATION IN WHICH THE AMIDE NITROGEN HAS BEEN REPLACED WITH A CH2, MAKING THE NORMAL AMIDE BOND BETWEEN THESE TWO RESIDUES A KETONE BOND. THE FIBRINOPEPTIDE NUMBERING IS CONSEQUENTLY INCREMENTED BY 1 AFTER THIS RESIDUE IN KEEPING WITH THE FIBRINOGEN NUMBERING SCHEME. THERE ARE ALTERNATE CONFORMATIONS FOR RESIDUES PRO 18 AND ARG 19 IN FIBRINOPEPTIDE III. Source: (natural) ![]() ![]() |
#5: Protein | Mass: 29772.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 1 types, 733 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
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-Details
Sequence details | CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ...CHYMOTRYPS |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.73 % |
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop / Details: Martin, P.D., (1992) J. Biol. Chem., 267, 7911. |
Components of the solutions | *PLUS Conc.: 40 % / Common name: ammonium sulfate |
-Data collection
Detector | Type: SIEMENS / Detector: X1000 MULTIWIRE |
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Reflection | Resolution: 2.2→7 Å / Num. obs: 45875 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.2→2.3 Å / Rsym value: 0.072 / % possible all: 15 |
Reflection | *PLUS Num. measured all: 117995 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 15 % |
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Processing
Software |
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Refinement | Resolution: 2.2→7 Å / Rfactor Rwork: 0.171 / Rfactor obs: 0.171 / σ(F): 1 Details: THERE ARE THREE INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX I IS EPSILON THROMBIN (ADDITIONAL CHAIN BREAK BETWEEN RESIDUES 149A AND 149B), AND MOLECULES II AND III ARE ALPHA ...Details: THERE ARE THREE INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX I IS EPSILON THROMBIN (ADDITIONAL CHAIN BREAK BETWEEN RESIDUES 149A AND 149B), AND MOLECULES II AND III ARE ALPHA THROMBIN. FIBRINOPEPTIDES I AND II HAVE OCCUPANCIES THAT MAKES THE AVERAGE SIDE CHAIN B OF OPR-16 ROUGHLY EQUAL TO THAT IN FIBRINOPEPTIDE III. THE DEPOSITORS DO NOT SEE ANY DENSITY AT ALL FOR THROMBIN RESIDUES 1U - 1I, AND POOR DENSITY FOR THE N AND C TERMINI OF THE LIGHT CHAINS, THE C TERMINUS OF THE HEAVY CHAINS, AND THE FIVE RESIDUES BORDERING 149B IN MOLECULES II AND III. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati sigma a obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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