MolNFT v1 · #186985 · protein
Crystal structure of a fe-bound RIDC1 variant in the presence of reductant
7RWY · Soluble cytochrome B562: “Crystal structure of a fe-bound RIDC1 variant in the presence of reductant”. X-ray diffraction, 2 ligands (HEC, FE), 11 pockets (best druggability 0.79). MolNFT v1 #186985 on GenesisL1: 3D structure…
- PDB
- 7RWY
- Type
- protein
- Length
- 636 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEC, FE
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Soluble cytochrome B562 | protein | 106 | 79% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEC · Heme C · ligand · 6 copies · chains A, B, C, D, E, F
- FE · Fe (III) ion · metal · 4 copies · chains B, C, F, A, D, E
- 1PE · Pentaethylene glycol · additive · 2 copies · chains B, C, F, A, D, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.79 | 0.83 | 62 | HEC, TRS |
| 2 | 470 | 0.78 | 0.86 | 60 | HEC |
| 3 | 756 | 0.74 | 0.79 | 64 | 1PE |
| 4 | 131 | 0.71 | 0.91 | 24 | empty |
| 5 | 587 | 0.69 | 0.78 | 46 | 1PE |
Interfaces
7 interfaces between chains.
- B–C · 807 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 739 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 646 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 636 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 392 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 cofactor (heme c attachment).
Compared structures
- 7RWY · Crystal structure of a Fe-bound RIDC1 variant in the presence of reductant · the same entry in another collection · chain F against F, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 P0ABE7
- Elsewhere: RCSB PDB 7RWY · PDBe 7RWY · UniProt P0ABE7
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