Research workbench
Crystal structure of thrombin in complex with COMPOUND51
Analyse Crystal structure of thrombin in complex with COMPOUND51 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZV8
- Type
- protein
- Length
- 288 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Hirudin-2
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- QQT, NAG
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 250 | 14% helix, 36% strand | P00734 |
| I | Hirudin-2 | protein | 11 | 27% helix, 0% strand | P28504 |
Ligands and binding sites
- QQT · [2-[[(1~{S})-1-(3-chlorophenyl)-2-fluoranyl-ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{S}, 5~{S})-5-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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 | 298 | 0.61 | 0.79 | 40 | QQT |
Interfaces
2 interfaces between chains.
- L–H · 1074 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 625 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 6ZV8 · Crystal Structure of Thrombin in complex with compound51 · 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 P28504
- Elsewhere: RCSB PDB 6ZV8 · PDBe 6ZV8 · UniProt P00734 · UniProt P28504
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