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Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence GLU666-GLU672 for processing at the heavy chain-B domain junction
Analyse Structural basis of thrombin-mediated factor V activation: essential role of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P70
- Type
- protein
- Length
- 1,144 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human alpha-thrombin, light chain; Human alpha-thrombin, heavy chain; Human factor V…
- EC
- 3.4.21.5
- UniProt
- P00734, P12259
- Ligands
- BEN, NAG, BGC, NA
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 9 distinct chains · 15% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Human alpha-thrombin, light chain (EC 3.4.21.5) | protein | 29 | 41% helix, 0% strand | P00734 |
| B | Human alpha-thrombin, heavy chain (EC 3.4.21.5) | protein | 252 | 15% helix, 36% strand | P00734 |
| D | Human alpha-thrombin, heavy chain (EC 3.4.21.5) | protein | 250 | 14% helix, 36% strand | P00734 |
| F | Human alpha-thrombin, heavy chain (EC 3.4.21.5) | protein | 252 | 14% helix, 34% strand | P00734 |
| G | Human alpha-thrombin, light chain (EC 3.4.21.5) | protein | 28 | 32% helix, 0% strand | P00734 |
| H | Human alpha-thrombin, heavy chain (EC 3.4.21.5) | protein | 254 | 14% helix, 33% strand | P00734 |
| M | Human factor V, A2-B domain linker | protein | 6 | 0% helix, 0% strand | P12259 |
| N, O | Human factor V, A2-B domain linker | protein | 5 | 0% helix, 0% strand | P12259 |
| P | Human factor V, A2-B domain linker | protein | 5 | 0% helix, 0% strand | P12259 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 4 copies · chains B, D, F, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains F, H, B, D
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains B, F, H
- NA · Sodium ion · metal · 7 copies · chains B, C, D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.78 | 0.82 | 61 | BEN |
| 2 | 805 | 0.77 | 0.80 | 62 | BEN |
| 3 | 668 | 0.76 | 0.82 | 63 | BEN |
| 4 | 218 | 0.54 | 0.77 | 37 | BEN |
| 5 | 179 | 0.45 | 0.74 | 22 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1090 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1087 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1077 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1062 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 459 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3P70 · Structural basis of thrombin-mediated factor V activation: essential role of the… · the same entry in another collection · chain P against P, 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
- Every structure of UniProt P12259
- Elsewhere: RCSB PDB 3P70 · PDBe 3P70 · UniProt P00734 · UniProt P12259
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