MolNFT v1 · #141843 · protein
Crystal structure of dfa-iiiase from arthrobacter chlorophenolicus A6 in complex with dfa-III
5ZKU: “Crystal structure of dfa-iiiase from arthrobacter chlorophenolicus A6 in complex with dfa-III”. X-ray diffraction, 1 ligand (9F3), 20 pockets (best druggability 0.86). MolNFT v1 #141843 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ZKU
- Type
- protein
- Length
- 2,653 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dfa-iiiase
- EC
- 3.2.1.-
- UniProt
- B8HDZ1
- Ligands
- 9F3
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dfa-iiiase (EC 3.2.1.-) | protein | 442 | 12% helix, 40% strand | B8HDZ1 |
| B, C, D, E | Dfa-iiiase (EC 3.2.1.-) | protein | 442 | 12% helix, 39% strand | B8HDZ1 |
| F | Dfa-iiiase (EC 3.2.1.-) | protein | 443 | 13% helix, 39% strand | B8HDZ1 |
Ligands and binding sites
- 9F3 · (2r,3's,4's,4ar,5'r,6r,7r,7as)-4A,5',6-tris(hydroxymethyl)spiro[3,6,7,7a-tetrahydrofuro[2,3-b][1,4]dioxine-2,2'-oxolane]-3',4',7-triol · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.86 | 0.88 | 97 | empty |
| 2 | 146 | 0.82 | 0.98 | 26 | 9F3 |
| 3 | 484 | 0.81 | 0.88 | 54 | empty |
| 4 | 137 | 0.81 | 0.98 | 30 | 9F3 |
| 5 | 140 | 0.81 | 0.98 | 31 | 9F3 |
Interfaces
9 interfaces between chains.
- D–F · 2969 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2950 Ų buried · 55 hydrogen bonds · protein-protein
- D–E · 2948 Ų buried · 51 hydrogen bonds · protein-protein
- E–F · 2947 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 2934 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 5ZKU · Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 in complex with… · 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 B8HDZ1
- Elsewhere: RCSB PDB 5ZKU · PDBe 5ZKU · UniProt B8HDZ1
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