MolNFT v1 · #188396 · protein
Cryo-EM structure of human prothrombinase on a nanodisc at 5.3 ångström resolution
7TPQ · Factor X light chain: “Cryo-EM structure of human prothrombinase on a nanodisc at 5.3 ångström resolution”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #188396 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7TPQ
- Type
- protein
- Length
- 1,743 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Factor X light chain; Coagulation factor va; Activated factor xa heavy chain
- UniProt
- P00742, P12259
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 5% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Factor X light chain | protein | 139 | 19% helix, 4% strand | P00742 |
| C | Coagulation factor va | protein | 709 | 6% helix, 18% strand | P12259 |
| D | Coagulation factor va | protein | 641 | 2% helix, 24% strand | P12259 |
| B | Activated factor xa heavy chain | protein | 254 | 4% helix, 16% strand | P00742 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.85 | 0.95 | 44 | empty |
| 2 | 1193 | 0.85 | 0.86 | 129 | empty |
| 3 | 712 | 0.81 | 0.85 | 94 | empty |
| 4 | 462 | 0.79 | 0.86 | 67 | empty |
| 5 | 105 | 0.77 | 0.97 | 35 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2718 Ų buried · 30 hydrogen bonds · protein-protein
- C–B · 1336 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 681 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 369 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 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 P00742
- Every structure of UniProt P12259
- Elsewhere: RCSB PDB 7TPQ · PDBe 7TPQ · UniProt P00742 · UniProt P12259
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