MolNFT v1 · #74788 · protein
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
3P6Z · Thrombin light chain: “Structural basis of thrombin mediated factor V activation: essential role of the hirudin-like sequence…”. X-ray diffraction, 4 ligands (0G6, NAG, NA), 6 pockets (best druggability 0.56). MolNFT v1 #74788 on…
- PDB
- 3P6Z
- Type
- protein
- Length
- 584 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Coagulation factor V
- EC
- 3.4.21.5
- UniProt
- P00734, P12259
- Ligands
- 0G6, NAG, NA, CL
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 30 | 40% helix, 0% strand | P00734 |
| B, H | Thrombin heavy chain (EC 3.4.21.5) | protein | 255 | 15% helix, 34% strand | P00734 |
| C | Coagulation factor V | protein | 7 | 0% helix, 0% strand | P12259 |
| G | Thrombin light chain (EC 3.4.21.5) | protein | 29 | 41% helix, 0% strand | P00734 |
| I | Coagulation factor V | protein | 8 | 0% helix, 0% strand | P12259 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · 2 copies · chains B, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, H
- NA · Sodium ion · metal · 9 copies · chains A, B, G, H
- CL · Chloride ion · ion · 3 copies · chains B, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.56 | 0.77 | 41 | 0G6 |
| 2 | 221 | 0.56 | 0.78 | 39 | 0G6 |
| 3 | 209 | 0.48 | 0.75 | 26 | CL |
| 4 | 180 | 0.45 | 0.74 | 32 | empty |
| 5 | 54 | 0.36 | 0.79 | 15 | MPD |
Interfaces
5 interfaces between chains.
- A–B · 1162 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1085 Ų buried · 29 hydrogen bonds · protein-protein
- B–H · 461 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 449 Ų buried · 4 hydrogen bonds · protein-protein
- H–I · 437 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 3P6Z · Structural basis of thrombin mediated factor V activation: essential role of the… · the same entry in another collection · chain C against C, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain B against A, TM-score 0.92
- P12259 · AlphaFold monomer V2.0 prediction for coagulation factor V (P12259) · a predicted model of the same protein · chain C against A, TM-score 0.57
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 3P6Z · PDBe 3P6Z · UniProt P00734 · UniProt P12259
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