MolNFT v1 · #166945 · protein
Crystal structure of human thrombin bound to ppack with tryptophans replaced by 5-F-tryptophan
6V64 · Thrombin light chain: “Crystal structure of human thrombin bound to ppack with tryptophans replaced by 5-F-tryptophan”. X-ray diffraction, 2 ligands (0G6, NA), 1 pocket (best druggability 0.60). MolNFT v1 #166945 on GenesisL1: 3D…
- PDB
- 6V64
- Type
- protein
- Length
- 281 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, NA
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 29 | 38% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 252 | 13% helix, 35% strand | P00734 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · chains B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.60 | 0.81 | 39 | 0G6 |
Interfaces
1 interface between chains.
- A–B · 1116 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified, 4 disulfide, 2 covalent (nonstandard, disulfide, covalent ligand).
Compared structures
- 6V64 · Crystal structure of human thrombin bound to ppack with tryptophans replaced by… · the same entry in another collection · chain A against A, 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
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
- Elsewhere: RCSB PDB 6V64 · PDBe 6V64 · UniProt P00734
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.