Research workbench
Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- CARBAMIMIDOYLPHENYL)METHYLAMINO)-2-oxo-butyl)-3-phenyl-propanamide
Analyse Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UFE
- Type
- protein
- Length
- 290 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
- 3ZD, NAG, NA, PO4
- Pockets
- 2 · 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 | 251 | 16% helix, 35% strand | P00734 |
| I | Hirudin variant-2 | protein | 11 | 27% helix, 0% strand | P09945 |
| L | Thrombin light chain (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
Ligands and binding sites
- 3ZD · (2R)-N-[(2S)-1-[(4-carbamimidoylphenyl)methylamino]-1-oxidanylidene-propan-2-yl]-3-phenyl-2-[(phenylmethyl)sulfonylamino]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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.55 | 0.77 | 36 | 3ZD |
| 2 | 52 | 0.28 | 0.75 | 12 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1112 Ų buried · 29 hydrogen bonds · protein-protein
- H–I · 624 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 4UFE · 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 4UFE · PDBe 4UFE · UniProt P00734 · UniProt P09945
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