MolNFT v1 · #141845 · protein
Crystal structure of dfa-iiiase from arthrobacter chlorophenolicus A6 in complex with GF2
5ZKW: “Crystal structure of dfa-iiiase from arthrobacter chlorophenolicus A6 in complex with GF2”. X-ray diffraction, 2 ligands (FRU, GLC), 20 pockets (best druggability 0.86). MolNFT v1 #141845 on GenesisL1: 3D structure, binding sites…
- PDB
- 5ZKW
- Type
- protein
- Length
- 2,545 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
- FRU, GLC
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dfa-iiiase (EC 3.2.1.-) | protein | 417 | 11% helix, 41% strand | B8HDZ1 |
| B | Dfa-iiiase (EC 3.2.1.-) | protein | 422 | 10% helix, 41% strand | B8HDZ1 |
| D | Dfa-iiiase (EC 3.2.1.-) | protein | 438 | 12% helix, 40% strand | B8HDZ1 |
| C | Dfa-iiiase (EC 3.2.1.-) | protein | 412 | 10% helix, 40% strand | B8HDZ1 |
| E | Dfa-iiiase (EC 3.2.1.-) | protein | 436 | 12% helix, 40% strand | B8HDZ1 |
| F | Dfa-iiiase (EC 3.2.1.-) | protein | 420 | 11% helix, 41% strand | B8HDZ1 |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 8 copies · chains A, B, D, C, E, F
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, D, C, 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 | 790 | 0.86 | 0.89 | 84 | empty |
| 2 | 166 | 0.82 | 0.97 | 31 | empty |
| 3 | 552 | 0.80 | 0.87 | 60 | empty |
| 4 | 524 | 0.80 | 0.87 | 55 | empty |
| 5 | 114 | 0.79 | 0.98 | 30 | empty |
Interfaces
9 interfaces between chains.
- E–F · 2930 Ų buried · 53 hydrogen bonds · protein-protein
- A–D · 2908 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 2632 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2596 Ų buried · 49 hydrogen bonds · protein-protein
- C–F · 2591 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 5ZKW · Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 in complex with GF2 · the same entry in another collection · chain F against F, 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 5ZKW · PDBe 5ZKW · UniProt B8HDZ1
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