MolNFT v1 · #110867 · protein
Crystal structure of caenorhabditis elegans acdh-11 in complex with C11-CoA
4Y9J · Protein acdh-11, isoform B: “Crystal structure of caenorhabditis elegans acdh-11 in complex with C11-CoA”. X-ray diffraction, 2 ligands (FAD, UCC), 14 pockets (best druggability 0.84). MolNFT v1 #110867 on GenesisL1: 3D structure…
- PDB
- 4Y9J
- Type
- protein
- Length
- 1,185 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein acdh-11, isoform B
- EC
- 1.3.8.9
- UniProt
- Q3T978
- Ligands
- FAD, UCC
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein acdh-11, isoform B (EC 1.3.8.9) | protein | 592 | 56% helix, 13% strand | Q3T978 |
| B | Protein acdh-11, isoform B (EC 1.3.8.9) | protein | 593 | 56% helix, 13% strand | Q3T978 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- UCC · S-{(3S,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} undecanethioate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.84 | 0.86 | 111 | FAD, UCC |
| 2 | 1060 | 0.84 | 0.85 | 70 | empty |
| 3 | 1048 | 0.84 | 0.85 | 121 | FAD, UCC |
| 4 | 106 | 0.44 | 0.78 | 31 | empty |
| 5 | 67 | 0.43 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4731 Ų buried · 96 hydrogen bonds · protein-protein
Compared structures
- 4Y9J · Crystal Structure of Caenorhabditis elegans ACDH-11 in complex with C11-CoA · the same entry in another collection · chain A against A, 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 Q3T978
- Elsewhere: RCSB PDB 4Y9J · PDBe 4Y9J · UniProt Q3T978
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