MolNFT v1 · #107606 · protein
Thrombin in complex with 4-(((1-((2S)-1-((2R)-2-(benzylsulfonylamino)- 3-phenyl-PROPANOYL)PYRROLIDIN-2-yl)-1-oxo-ETHYL)AMINO)METHYL) benzamidine
4UFD · Thrombin heavy chain: “Thrombin in complex with 4-(((1-((2S)-1-((2R)-2-(benzylsulfonylamino)…”. X-ray diffraction, 4 ligands (S49, NAG, NA), 1 pocket (best druggability 0.55). MolNFT v1 #107606 on GenesisL1: 3D structure, binding…
- PDB
- 4UFD
- Type
- protein
- Length
- 281 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin heavy chain; Hirudin variant-2; Thrombin light chain
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- S49, NAG, NA, PO4
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 14% helix, 36% strand | P00734 |
| I | Hirudin variant-2 | protein | 3 | 0% helix, 0% strand | P09945 |
| L | Thrombin light chain (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
Ligands and binding sites
- S49 · (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-3-phenyl-2-[(phenylmethyl)sulfonylamino]propanoyl]pyrrolidine-2-carboxamide · 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
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 | 248 | 0.55 | 0.77 | 37 | S49 |
Interfaces
2 interfaces between chains.
- H–L · 1099 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 277 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 4UFD · Thrombin in complex with 4-(((1-((2S)-1-((2R)-2-(benzylsulfonylamino)… · the same entry in another collection · chain H against H, 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 4UFD · PDBe 4UFD · UniProt P00734 · UniProt P09945
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