MolNFT v1 · #188395 · protein
Cryo-EM structure of human PROTHROMBIN:PROTHROMBINASE at 4.1 ångström resolution
7TPP: “Cryo-EM structure of human PROTHROMBIN:PROTHROMBINASE at 4.1 ångström resolution”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #188395 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7TPP
- Type
- protein
- Length
- 2,309 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Factor X light chain; Coagulation factor va; Activated factor xa heavy chain
- EC
- 3.4.21.5
- UniProt
- P00734, P00742, P12259
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 5% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Prothrombin (EC 3.4.21.5) | protein | 566 | 5% helix, 10% strand | P00734 |
| A | Factor X light chain | protein | 139 | 19% helix, 3% strand | P00742 |
| C | Coagulation factor va | protein | 709 | 6% helix, 20% strand | P12259 |
| D | Coagulation factor va | protein | 641 | 1% helix, 24% strand | P12259 |
| B | Activated factor xa heavy chain | protein | 254 | 5% helix, 15% strand | P00742 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.84 | 0.85 | 91 | empty |
| 2 | 675 | 0.83 | 0.87 | 93 | empty |
| 3 | 1112 | 0.82 | 0.83 | 127 | empty |
| 4 | 187 | 0.80 | 0.95 | 36 | empty |
| 5 | 240 | 0.79 | 0.91 | 36 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2782 Ų buried · 30 hydrogen bonds · protein-protein
- E–C · 1335 Ų buried · 18 hydrogen bonds · protein-protein
- C–B · 1325 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 687 Ų buried · 9 hydrogen bonds · protein-protein
- E–B · 668 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 7TPP · Cryo-em structure of human prothrombin:prothrombinase at 4.1 Angstrom resolution · the same entry in another collection · chain B against B, TM-score 1.00
- P12259 · AlphaFold monomer V2.0 prediction for coagulation factor V (P12259) · a predicted model of the same protein · chain D against A, TM-score 0.89
- P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain B against A, TM-score 0.83
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 P00742
- Every structure of UniProt P12259
- Elsewhere: RCSB PDB 7TPP · PDBe 7TPP · UniProt P00734 · UniProt P00742 · UniProt P12259
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