Research workbench
Stigmatellin and antimycin bound cytochrome BC1 complex from chicken
Analyse Stigmatellin and antimycin bound cytochrome BC1 complex from chicken in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H1I
- Type
- protein
- Length
- 4,069 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinol-cytochrome-C reductase complex core protein I, mitochondrial…
- EC
- 1.10.2.2
- UniProt
- P18946, Q5ZLR5
- Ligands
- PEE, HEM, CDL, HEC, FES, SMA, ANY, PLC, UNL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 17 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquinol-cytochrome-C reductase complex core protein I, mitochondrial (EC 1.10.2.2) | protein | 443 | 45% helix, 18% strand | — |
| B | Ubiquinol-cytochrome-C reductase complex core protein 2, mitochondrial (EC 1.10.2.2) | protein | 421 | 41% helix, 17% strand | — |
| C | Cytochrome B (EC 1.10.2.2) | protein | 380 | 73% helix, 2% strand | P18946 |
| D, Q | Cytochrome C1, heme protein, mitochondrial (EC 1.10.2.2) | protein | 241 | 41% helix, 8% strand | — |
| E, R | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 196 | 22% helix, 19% strand | Q5ZLR5 |
| F, S | Ubiquinol-cytochrome C reductase complex 14 kda protein (EC 1.10.2.2) | protein | 101 | 71% helix, 0% strand | — |
| G | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 81 | 57% helix, 11% strand | — |
| H | Ubiquinol-cytochrome C reductase complex 11 kda protein (EC 1.10.2.2) | protein | 70 | 64% helix, 0% strand | — |
| I | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 46 | 9% helix, 15% strand | Q5ZLR5 |
| J | Ubiquinol-cytochrome C reductase complex 7.2 kda protein (EC 1.10.2.2) | protein | 61 | 77% helix, 0% strand | — |
| N | Ubiquinol-cytochrome-C reductase complex core protein I, mitochondrial (EC 1.10.2.2) | protein | 442 | 45% helix, 18% strand | — |
| O | Ubiquinol-cytochrome-C reductase complex core protein 2, mitochondrial (EC 1.10.2.2) | protein | 422 | 41% helix, 19% strand | — |
| P | Cytochrome B (EC 1.10.2.2) | protein | 379 | 72% helix, 2% strand | P18946 |
| T | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 79 | 58% helix, 11% strand | — |
| U | Ubiquinol-cytochrome C reductase complex 11 kda protein (EC 1.10.2.2) | protein | 67 | 67% helix, 0% strand | — |
| V | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 43 | 7% helix, 16% strand | Q5ZLR5 |
| W | Ubiquinol-cytochrome C reductase complex 7.2 kda protein (EC 1.10.2.2) | protein | 59 | 80% helix, 0% strand | — |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 6 copies · chains A, C, D, E, J, F, G, N, P, Q, R, W, S, T
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, P
- CDL · Cardiolipin · ligand · 4 copies · chains C, D, F, G, P, Q, S, T
- HEC · Heme C · ligand · 2 copies · chains D, Q
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, R
- SMA · Stigmatellin A · ligand · 2 copies · chains C, R, E, P
- ANY · 2-methyl-butyric acid 3-(3-formylamino-2-hydroxy-benzoylamino)-8-heptyl-2,6-dimethyl-4,9-dioxo-[1,5]dioxonan-7-yl ester · ligand · 2 copies · chains C, P
- PLC · Diundecyl phosphatidyl choline · ligand · 2 copies · chains C, D, E, J, P, Q, R, W
- UNL · Unknown ligand · ion · 10 copies · chains C, P, R, E, A, B
- GOL · Glycerol · additive · 2 copies · chains C, D, P, Q
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 | 442 | 0.85 | 0.92 | 48 | HEM, UNL |
| 2 | 782 | 0.84 | 0.87 | 82 | HEM, UNL, GOL |
| 3 | 458 | 0.80 | 0.87 | 48 | HEM, UNL, ANY |
| 4 | 113 | 0.79 | 0.98 | 26 | empty |
| 5 | 718 | 0.79 | 0.83 | 72 | HEM, ANY, UNL |
Interfaces
57 interfaces between chains.
- A–B · 2035 Ų buried · 36 hydrogen bonds · protein-protein
- N–O · 2025 Ų buried · 34 hydrogen bonds · protein-protein
- O–V · 1762 Ų buried · 18 hydrogen bonds · protein-protein
- B–I · 1729 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1647 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 cofactor (disulfide, heme c attachment).
Compared structures
- 3H1I · Stigmatellin and antimycin bound cytochrome bc1 complex from chicken · the same entry in another collection · chain H against H, 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 P18946
- Every structure of UniProt Q5ZLR5
- Elsewhere: RCSB PDB 3H1I · PDBe 3H1I · UniProt P18946 · UniProt Q5ZLR5
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