Research workbench
Structure of 4-hydroxybenzoyl-CoA reductase from thauera aromatica
Analyse Structure of 4-hydroxybenzoyl-CoA reductase from thauera aromatica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RM6
- Type
- protein
- Length
- 2,481 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxybenzoyl-CoA reductase alpha subunit; 4-hydroxybenzoyl-CoA reductase beta…
- EC
- 1.3.99.20
- UniProt
- O33819, O33820, O33818
- Ligands
- FES, PCD, FAD, SF4, NA, K, CL, SO4
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxybenzoyl-CoA reductase alpha subunit (EC 1.3.99.20) | protein | 761 | 31% helix, 26% strand | O33819 |
| B, E | 4-hydroxybenzoyl-CoA reductase beta subunit (EC 1.3.99.20) | protein | 323 | 31% helix, 23% strand | O33820 |
| C, F | 4-hydroxybenzoyl-CoA reductase gamma subunit (EC 1.3.99.20) | protein | 157 | 41% helix, 20% strand | O33818 |
| D | 4-hydroxybenzoyl-CoA reductase alpha subunit (EC 1.3.99.20) | protein | 760 | 31% helix, 26% strand | O33819 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, C, D, F
- PCD · (molybdopterin-cytosine dinucleotide-S,S)-dioxo-aqua-molybdenum(v) · ligand · 2 copies · chains A, C, D, F
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, C, D, E, F
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, E
- NA · Sodium ion · metal · 2 copies · chains A, D
- K · Potassium ion · metal · chains D
- CL · Chloride ion · ion · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · chains D, F
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.83 | 0.84 | 93 | FAD |
| 2 | 490 | 0.82 | 0.89 | 71 | PCD, EPE |
| 3 | 946 | 0.82 | 0.84 | 99 | FAD |
| 4 | 562 | 0.82 | 0.88 | 71 | empty |
| 5 | 636 | 0.82 | 0.87 | 78 | SO4 |
Interfaces
10 interfaces between chains.
- A–D · 2075 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 2019 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 2019 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1631 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1628 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1RM6 · Structure of 4-hydroxybenzoyl-CoA reductase from Thauera aromatica · the same entry in another collection · chain F against F, TM-score 1.00
- O33819 · AlphaFold monomer V2.0 prediction for 4-hydroxybenzoyl-CoA reductase subunit alpha… · a predicted model of the same protein · chain A against A, TM-score 1.00
- O33818 · AlphaFold monomer V2.0 prediction for 4-hydroxybenzoyl-CoA reductase subunit gamma… · a predicted model of the same protein · chain C against A, TM-score 1.00
- O33820 · AlphaFold monomer V2.0 prediction for 4-hydroxybenzoyl-CoA reductase subunit beta (O33820) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O33819
- Every structure of UniProt O33820
- Every structure of UniProt O33818
- Elsewhere: RCSB PDB 1RM6 · PDBe 1RM6 · UniProt O33819 · UniProt O33820 · UniProt O33818
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