MolNFT v1 · #105003 · protein
Crystal structure of dihydroxybenzoic acid decarbboxylase BPRO_2061 (target efi-500288) from polaromonas sp. JS666 with bound manganese and an inhibitor, 2-nitroresorcinol
4QRO · Gamma-resorcylate decarboxylase: “Crystal structure of dihydroxybenzoic acid decarbboxylase BPRO_2061 (target efi-500288) from polaromonas sp.…”. X-ray diffraction, 3 ligands (38L, BCT, MN), 20 pockets (best druggability 0.78).…
- PDB
- 4QRO
- Type
- protein
- Length
- 2,603 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-resorcylate decarboxylase
- UniProt
- Q12BV1
- Ligands
- 38L, BCT, MN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-resorcylate decarboxylase | protein | 332 | 52% helix, 12% strand | Q12BV1 |
| B, F, H | Gamma-resorcylate decarboxylase | protein | 324 | 52% helix, 12% strand | Q12BV1 |
| C | Gamma-resorcylate decarboxylase | protein | 325 | 53% helix, 12% strand | Q12BV1 |
| D | Gamma-resorcylate decarboxylase | protein | 323 | 52% helix, 12% strand | Q12BV1 |
| E | Gamma-resorcylate decarboxylase | protein | 324 | 52% helix, 13% strand | Q12BV1 |
| G | Gamma-resorcylate decarboxylase | protein | 327 | 51% helix, 12% strand | Q12BV1 |
Ligands and binding sites
- 38L · 2-nitrobenzene-1,3-diol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- BCT · Bicarbonate ion · ligand · chains G, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- ACT · Acetate ion · additive · 11 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 6 copies · chains A, D, B, C, F, G, E, H
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 | 98 | 0.78 | 0.98 | 28 | empty |
| 2 | 98 | 0.77 | 0.98 | 29 | empty |
| 3 | 97 | 0.77 | 0.98 | 24 | empty |
| 4 | 92 | 0.76 | 0.98 | 29 | empty |
| 5 | 66 | 0.73 | 0.98 | 19 | ACT |
Interfaces
13 interfaces between chains.
- E–F · 3237 Ų buried · 43 hydrogen bonds · protein-protein
- G–H · 3215 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 3178 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 3175 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 551 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4QRO · CRYSTAL STRUCTURE of DIHYDROXYBENZOIC ACID DECARBBOXYLASE BPRO_2061 (TARGET EFI-500288)… · 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 Q12BV1
- Elsewhere: RCSB PDB 4QRO · PDBe 4QRO · UniProt Q12BV1
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