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Crystal structure of the anticoagulant slow form of thrombin
Analyse Crystal structure of the anticoagulant slow form of thrombin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SGI
- Type
- protein
- Length
- 561 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin (EC 3.4.21.5) | protein | 32 | 31% helix, 0% strand | P00734 |
| B | Thrombin (EC 3.4.21.5) | protein | 251 | 14% helix, 35% strand | P00734 |
| D | Thrombin (EC 3.4.21.5) | protein | 28 | 43% helix, 0% strand | P00734 |
| E | Thrombin (EC 3.4.21.5) | protein | 250 | 13% helix, 35% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.59 | 0.77 | 44 | empty |
| 2 | 213 | 0.54 | 0.78 | 34 | empty |
| 3 | 123 | 0.41 | 0.75 | 20 | empty |
| 4 | 71 | 0.35 | 0.77 | 19 | empty |
| 5 | 77 | 0.29 | 0.72 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1214 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1125 Ų buried · 27 hydrogen bonds · protein-protein
- B–E · 670 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 212 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1SGI · Crystal structure of the anticoagulant slow form of thrombin · the same entry in another collection · chain E against E, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00734
- Elsewhere: RCSB PDB 1SGI · PDBe 1SGI · UniProt P00734
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