MolNFT v1 · #141855 · protein
Crystal structure of mutant C387A of dfa-iiiase from arthrobacter chlorophenolicus A6 in complex with dfa-III
5ZLA · Dfa-iiiase C387A mutant: “Crystal structure of mutant C387A of dfa-iiiase from arthrobacter chlorophenolicus A6 in complex with dfa-III”. X-ray diffraction, 1 ligand (9F3), 20 pockets (best druggability 0.84). MolNFT v1 #141855 on…
- PDB
- 5ZLA
- Type
- protein
- Length
- 2,627 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dfa-iiiase C387A mutant
- EC
- 3.2.1.-
- UniProt
- B8HDZ1
- Ligands
- 9F3
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dfa-iiiase C387A mutant (EC 3.2.1.-) | protein | 439 | 13% helix, 39% strand | B8HDZ1 |
| B | Dfa-iiiase C387A mutant (EC 3.2.1.-) | protein | 441 | 12% helix, 40% strand | B8HDZ1 |
| C | Dfa-iiiase C387A mutant (EC 3.2.1.-) | protein | 438 | 13% helix, 40% strand | B8HDZ1 |
| D | Dfa-iiiase C387A mutant (EC 3.2.1.-) | protein | 437 | 12% helix, 40% strand | B8HDZ1 |
| E, F | Dfa-iiiase C387A mutant (EC 3.2.1.-) | protein | 436 | 12% helix, 40% 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, D, B, C, F, E
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 | 1134 | 0.84 | 0.85 | 114 | empty |
| 2 | 548 | 0.83 | 0.89 | 59 | empty |
| 3 | 164 | 0.82 | 0.98 | 32 | 9F3 |
| 4 | 159 | 0.82 | 0.97 | 31 | 9F3 |
| 5 | 543 | 0.81 | 0.88 | 60 | empty |
Interfaces
9 interfaces between chains.
- B–D · 2972 Ų buried · 54 hydrogen bonds · protein-protein
- C–F · 2910 Ų buried · 53 hydrogen bonds · protein-protein
- C–E · 2908 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2900 Ų buried · 50 hydrogen bonds · protein-protein
- A–D · 2877 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 5ZLA · Crystal structure of mutant C387A of DFA-IIIase from Arthrobacter chlorophenolicus A6 in… · 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 5ZLA · PDBe 5ZLA · UniProt B8HDZ1
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