MolNFT v1 · #138630 · protein
Crystal structure of fragment 3-(3-(pyridin-2-YLMETHOXY)QUINOXALIN-2- YL)PROPANOIC acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
5WPB · Histone deacetylase 6: “Crystal structure of fragment 3-(3-(pyridin-2-YLMETHOXY)QUINOXALIN-2- YL)PROPANOIC acid bound in the…”. X-ray diffraction, 3 ligands (B8P, ZN, UNX). MolNFT v1 #138630 on GenesisL1: 3D structure, binding sites…
- PDB
- 5WPB
- Type
- protein
- Length
- 101 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase 6
- EC
- 3.5.1.98
- UniProt
- Q9UBN7
- Ligands
- B8P, ZN, UNX
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase 6 (EC 3.5.1.98) | protein | 101 | 26% helix, 18% strand | Q9UBN7 |
Ligands and binding sites
- B8P · 3-{3-[(pyridin-2-yl)methoxy]quinoxalin-2-yl}propanoic acid · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- UNX · Unknown atom or ion · ion · 17 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5WPB · Crystal structure of fragment 3-(3-(pyridin-2-ylmethoxy)quinoxalin-2-yl)propanoic acid… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBN7 · AlphaFold monomer V2.0 prediction for histone deacetylase 6 (Q9UBN7) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9UBN7
- Elsewhere: RCSB PDB 5WPB · PDBe 5WPB · UniProt Q9UBN7
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