Research workbench
Rhodobacter sphaeroides BC1 with stigmatellin a
Analyse Rhodobacter sphaeroides BC1 with stigmatellin a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NIN
- Type
- protein
- Length
- 5,178 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B; Cytochrome C1; Ubiquinol-cytochrome C reductase iron-sulfur subunit
- EC
- 1.10.2.2
- UniProt
- A0A344Q9J3, A0A344Q9J2, A0A344Q9J4
- Ligands
- HEM, SMA, HEC, FES, 6PE, SR
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, K, O, S, W | Cytochrome B | protein | 428 | 68% helix, 2% strand | A0A344Q9J3 |
| B, F, L, P, T, X | Cytochrome C1 | protein | 256 | 38% helix, 7% strand | A0A344Q9J2 |
| C, G, M, Q, U, Y | Ubiquinol-cytochrome C reductase iron-sulfur subunit (EC 1.10.2.2) | protein | 179 | 26% helix, 27% strand | A0A344Q9J4 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, E, K, O, S, W
- SMA · Stigmatellin A · ligand · 6 copies · chains A, G, C, E, K, Q, M, O, S, Y, U, W
- HEC · Heme C · ligand · 6 copies · chains B, F, L, P, T, X
- FES · Fe2/s2 (inorganic) cluster · ligand · 6 copies · chains C, G, M, Q, U, Y
- 6PE · 1,2-dihexanoyl-sn-glycero-3-phosphoethanolamine · ligand · 3 copies · chains A, E, W
- SR · Strontium ion · metal · 6 copies · chains B, F, L, P, T, X
- BOG · octyl beta-D-glucopyranoside · additive · 6 copies · chains A, B, E, F, K, L, O, P, S, T, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.89 | 0.91 | 115 | HEM, BOG |
| 2 | 1027 | 0.88 | 0.89 | 112 | HEM |
| 3 | 1158 | 0.87 | 0.88 | 119 | HEM, BOG |
| 4 | 1089 | 0.87 | 0.88 | 122 | HEM |
| 5 | 984 | 0.87 | 0.88 | 98 | HEM |
Interfaces
38 interfaces between chains.
- K–L · 2027 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2027 Ų buried · 20 hydrogen bonds · protein-protein
- W–X · 2019 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 2008 Ų buried · 19 hydrogen bonds · protein-protein
- S–T · 1994 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 cofactor (disulfide, heme c attachment).
Compared structures
- 6NIN · Rhodobacter sphaeroides bc1 with STIGMATELLIN A · 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 A0A344Q9J3
- Every structure of UniProt A0A344Q9J2
- Every structure of UniProt A0A344Q9J4
- Elsewhere: RCSB PDB 6NIN · PDBe 6NIN · UniProt A0A344Q9J3 · UniProt A0A344Q9J2 · UniProt A0A344Q9J4
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