Research workbench
Crystal structure of an engineered metal-free RIDC1 variant containing five disulfide bonds.
Analyse Crystal structure of an engineered metal-free RIDC1 variant containing five… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L31
- Type
- protein
- Length
- 419 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEC, NA
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Soluble cytochrome B562 | protein | 106 | 78% helix, 0% strand | P0ABE7 |
| C | Soluble cytochrome B562 | protein | 101 | 79% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.86 | 0.87 | 88 | empty |
| 2 | 196 | 0.72 | 0.89 | 32 | empty |
| 3 | 136 | 0.62 | 0.86 | 28 | empty |
| 4 | 197 | 0.62 | 0.82 | 30 | HEC |
| 5 | 157 | 0.59 | 0.82 | 23 | HEC |
Interfaces
6 interfaces between chains.
- C–D · 653 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 619 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 608 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 530 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 242 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 5 disulfide, 1 modified (heme c attachment, disulfide, oxidation).
Compared structures
- 5L31 · Crystal structure of an engineered metal-free RIDC1 variant containing five disulfide… · the same entry in another collection · chain C against C, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A 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 5L31 · PDBe 5L31 · UniProt P0ABE7
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