MolNFT v1 · #107608 · protein
Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- CARBAMIMIDOYLPHENYL)METHYLAMINO)-2-oxo-ethyl)-N-methyl-3-phenyl- propanamide
4UFF · Thrombin heavy chain: “Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4…”. X-ray diffraction, 4 ligands (6V2, NAG, NA), 1 pocket (best druggability 0.55). MolNFT v1 #107608 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4UFF
- Type
- protein
- Length
- 288 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
- 6V2, NAG, NA, PO4
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 250 | 15% helix, 36% strand | P00734 |
| I | Hirudin variant-2 | protein | 11 | 27% helix, 0% strand | P09945 |
| L | Thrombin light chain (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
Ligands and binding sites
- 6V2 · (2R)-2-(benzylsulfonylamino)-N-(2-((4-carbamimidoylphenyl)methylamino)-2-oxo-ethyl)-N-methyl-3-phenyl-propanamide · 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
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 | 269 | 0.55 | 0.76 | 38 | 6V2 |
Interfaces
2 interfaces between chains.
- H–L · 1093 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 639 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 4UFF · Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4… · 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 4UFF · PDBe 4UFF · UniProt P00734 · UniProt P09945
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