MolNFT v1 · #92725 · protein
Structure of Y257F variant of homoprotocatechuate 2,3-dioxygenase from B.FUSCUM in complex with hpca at 1.85 ang resolution
4GHD: “Structure of Y257F variant of homoprotocatechuate 2,3-dioxygenase from B.FUSCUM in complex with hpca at 1.85…”. X-ray diffraction, 4 ligands (DHY, FE2, CA), 20 pockets (best druggability 0.83). MolNFT v1 #92725 on GenesisL1: 3D…
- PDB
- 4GHD
- Type
- protein
- Length
- 1,432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoprotocatechuate 2,3-dioxygenase
- EC
- 1.13.11.15
- UniProt
- Q45135
- Ligands
- DHY, FE2, CA, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homoprotocatechuate 2,3-dioxygenase (EC 1.13.11.15) | protein | 356 | 17% helix, 34% strand | Q45135 |
| B, D | Homoprotocatechuate 2,3-dioxygenase (EC 1.13.11.15) | protein | 360 | 18% helix, 35% strand | Q45135 |
| C | Homoprotocatechuate 2,3-dioxygenase (EC 1.13.11.15) | protein | 356 | 17% helix, 35% strand | Q45135 |
Ligands and binding sites
- DHY · 2-(3,4-dihydroxyphenyl)acetic 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 · 3 copies · chains A, B, D
- P6G · Hexaethylene glycol · additive · 5 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.83 | 0.89 | 70 | empty |
| 2 | 607 | 0.83 | 0.88 | 70 | empty |
| 3 | 122 | 0.80 | 0.98 | 26 | empty |
| 4 | 64 | 0.73 | 0.98 | 26 | empty |
| 5 | 310 | 0.69 | 0.83 | 34 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1687 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 1673 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1657 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 1332 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 529 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4GHD · Structure of Y257F 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 4GHD · PDBe 4GHD · UniProt Q45135
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