MolNFT v1 · #77695 · protein
Human thrombin in complex with MI331
3RML · Thrombin light chain: “Human thrombin in complex with MI331”. X-ray diffraction, 4 ligands (M31, NAG, NA), 3 pockets (best druggability 0.56). MolNFT v1 #77695 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3RML
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin variant-2
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- M31, NAG, NA, PO4
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 16% helix, 35% strand | P00734 |
| I | Hirudin variant-2 | protein | 11 | 27% helix, 0% strand | P09945 |
Ligands and binding sites
- M31 · N-(benzylsulfonyl)glycyl-N-[2-(aminomethyl)-5-chlorobenzyl]-L-prolinamide · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- NA · Sodium ion · metal · 2 copies · chains H
- PO4 · Phosphate ion · ion · chains H
- GOL · Glycerol · additive · 2 copies · chains H
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 | 233 | 0.56 | 0.78 | 37 | M31, GOL |
| 2 | 68 | 0.31 | 0.74 | 13 | empty |
| 3 | 54 | 0.30 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1101 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 659 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 3RML · Human Thrombin in complex with MI331 · the same entry in another collection · chain L against L, 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 P09945
- Elsewhere: RCSB PDB 3RML · PDBe 3RML · UniProt P00734 · UniProt P09945
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