MolNFT v1 · #170551 · protein
Thrombin in complex with D-phe-pro-3-chloro-1,3-dihydroxybenzylamide derivative (13C)
6YB6: “Thrombin in complex with D-phe-pro-3-chloro-1,3-dihydroxybenzylamide derivative (13C)”. X-ray diffraction, 4 ligands (OJK, NAG, NA). MolNFT v1 #170551 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YB6
- Type
- protein
- Length
- 291 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P00734, P09945
- Ligands
- OJK, NAG, NA, PO4
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | — | protein | 28 | — | P00734 |
| H | — | protein | 250 | — | P00734 |
| I | — | protein | 11 | — | P09945 |
| D | — | protein | 2 | — | — |
Ligands and binding sites
- OJK · 2-(aminomethyl)-5-chloranyl-benzene-1,4-diol · ligand · chains H, D
- 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
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 6YB6 · Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c) · the same entry in another collection · chain L against L, TM-score 1.00
- P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · a predicted model of the same protein · chain I against A, TM-score 0.50
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 6YB6 · PDBe 6YB6 · UniProt P00734 · UniProt P09945
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