MolNFT v1 · #111042 · protein
Thrombin in complex with (S)-(4-chloro-2-((1-(5-methyl-1H-pyrrole-2- CARBONYL)PYRROLIDINE-2-CARBOXAMIDO)METHYL)PHENYL)METHANAMINIUM
4YES · Thrombin light chain: “Thrombin in complex with (S)-(4-chloro-2-((1-(5-methyl-1H-pyrrole-2…”. X-ray diffraction, 3 ligands (45S, NAG, MG), 3 pockets (best druggability 0.57). MolNFT v1 #111042 on GenesisL1: 3D structure, binding…
- PDB
- 4YES
- Type
- protein
- Length
- 292 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin
- EC
- 3.4.21.5
- UniProt
- P00734, P01050
- Ligands
- 45S, NAG, MG
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 29 | 34% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 252 | 15% helix, 35% strand | P00734 |
| H | Hirudin | protein | 11 | 36% helix, 0% strand | P01050 |
Ligands and binding sites
- 45S · N-[2-(aminomethyl)-5-chlorobenzyl]-1-[(5-methyl-1H-pyrrol-2-yl)carbonyl]-L-prolinamide · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- MG · Magnesium ion · metal · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.57 | 0.78 | 40 | 45S |
| 2 | 86 | 0.36 | 0.75 | 13 | empty |
| 3 | 54 | 0.31 | 0.76 | 11 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1154 Ų buried · 28 hydrogen bonds · protein-protein
- B–H · 662 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 4YES · Thrombin in complex with (S)-(4-chloro-2-((1-(5-methyl-1H-pyrrole-2-carbonyl)pyrrolidine-2… · the same entry in another collection · chain A against A, TM-score 1.00
- P01050 · AlphaFold monomer V2.0 prediction for hirudin variant-1 (P01050) · a predicted model of the same protein · chain H against A, TM-score 0.48
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 P01050
- Elsewhere: RCSB PDB 4YES · PDBe 4YES · UniProt P00734 · UniProt P01050
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