MolNFT v1 · #64959 · protein
Crystal structure of na-free thrombin in complex with thrombomodulin
3GIS · Prothrombin: “Crystal structure of na-free thrombin in complex with thrombomodulin”. X-ray diffraction, 2 ligands (CA, SO4), 12 pockets (best druggability 0.73). MolNFT v1 #64959 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3GIS
- Type
- protein
- Length
- 1,228 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Thrombomodulin
- EC
- 3.4.21.5
- UniProt
- P00734, P07204
- Ligands
- CA, SO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 13% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Prothrombin (EC 3.4.21.5) | protein | 46 | 35% helix, 0% strand | P00734 |
| B | Prothrombin (EC 3.4.21.5) | protein | 252 | 16% helix, 33% strand | P00734 |
| D | Prothrombin (EC 3.4.21.5) | protein | 252 | 16% helix, 33% strand | P00734 |
| F | Prothrombin (EC 3.4.21.5) | protein | 248 | 14% helix, 35% strand | P00734 |
| X | Thrombomodulin | protein | 113 | 4% helix, 43% strand | P07204 |
| Y | Thrombomodulin | protein | 113 | 4% helix, 35% strand | P07204 |
| Z | Thrombomodulin | protein | 112 | 4% helix, 41% strand | P07204 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains X, Y, Z
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.73 | 0.80 | 84 | empty |
| 2 | 394 | 0.72 | 0.83 | 60 | empty |
| 3 | 311 | 0.64 | 0.80 | 51 | empty |
| 4 | 368 | 0.61 | 0.77 | 54 | empty |
| 5 | 341 | 0.60 | 0.77 | 38 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1739 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1718 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 1690 Ų buried · 33 hydrogen bonds · protein-protein
- F–Z · 811 Ų buried · 12 hydrogen bonds · protein-protein
- B–X · 800 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide (disulfide).
Compared structures
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
- Every structure of UniProt P07204
- Elsewhere: RCSB PDB 3GIS · PDBe 3GIS · UniProt P00734 · UniProt P07204
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