MolNFT v1 · #111967 · protein
Structure of H200E variant of homoprotocatechuate 2,3-dioxygenase from B.FUSCUM in complex with 4-sulfonyl catechol at 1.70 ang resolution
4Z6R: “Structure of H200E variant of homoprotocatechuate 2,3-dioxygenase from B.FUSCUM in complex with 4-sulfonyl…”. X-ray diffraction, 4 ligands (4SX, FE2, CA), 20 pockets (best druggability 0.85). MolNFT v1 #111967 on GenesisL1: 3D…
- PDB
- 4Z6R
- Type
- protein
- Length
- 1,427 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoprotocatechuate 2,3-dioxygenase
- UniProt
- Q45135
- Ligands
- 4SX, FE2, CA, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homoprotocatechuate 2,3-dioxygenase | protein | 355 | 17% helix, 34% strand | Q45135 |
| B, D | Homoprotocatechuate 2,3-dioxygenase | protein | 359 | 18% helix, 35% strand | Q45135 |
| C | Homoprotocatechuate 2,3-dioxygenase | protein | 354 | 17% helix, 34% strand | Q45135 |
Ligands and binding sites
- 4SX · 3,4-dihydroxybenzenesulfonic acid · ligand · chains C
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- P6G · Hexaethylene glycol · additive · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.85 | 0.95 | 46 | empty |
| 2 | 374 | 0.84 | 0.93 | 47 | empty |
| 3 | 102 | 0.78 | 0.98 | 24 | empty |
| 4 | 63 | 0.72 | 0.98 | 27 | empty |
| 5 | 64 | 0.72 | 0.98 | 28 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1688 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 1666 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1663 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1340 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 532 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4Z6R · Structure of H200E variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum 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 Q45135
- Elsewhere: RCSB PDB 4Z6R · PDBe 4Z6R · UniProt Q45135
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