Research workbench
Chicken cytochrome BC1 complex with ascochlorin bound at qo and qi sites
Analyse Chicken cytochrome BC1 complex with ascochlorin bound at qo and qi sites in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H1L
- Type
- protein
- Length
- 4,069 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial ubiquinol-cytochrome-C reductase complex core protein I; Mitochondrial…
- EC
- 1.10.2.2
- UniProt
- P18946, Q5ZLR5
- Ligands
- PEE, HEM, 3H1, CDL, HEC, FES, UNL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 17 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial ubiquinol-cytochrome-C reductase complex core protein I (EC 1.10.2.2) | protein | 443 | 47% helix, 18% strand | — |
| B | Mitochondrial ubiquinol-cytochrome-C reductase complex core protein 2 (EC 1.10.2.2) | protein | 421 | 41% helix, 18% strand | — |
| C | Cytochrome B (EC 1.10.2.2) | protein | 380 | 69% helix, 2% strand | P18946 |
| D, Q | Mitochondrial cytochrome C1, heme protein (EC 1.10.2.2) | protein | 241 | 41% helix, 7% strand | — |
| E, R | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 196 | 24% helix, 17% strand | Q5ZLR5 |
| F, S | Mitochondrial ubiquinol-cytochrome C reductase 14 kda protein (EC 1.10.2.2) | protein | 101 | 68% helix, 1% strand | — |
| G | Mitochondrial ubiquinol-cytochrome C reductase ubiquinone- binding protein qp-C (EC 1.10.2.2) | protein | 81 | 53% helix, 11% strand | — |
| H | Mitochondrial ubiquinol-cytochrome C reductase 11 kda protein, complex III subunit VIII (EC 1.10.2.2) | protein | 70 | 69% helix, 0% strand | — |
| I | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 46 | 9% helix, 11% strand | Q5ZLR5 |
| J | Mitochondrial ubiquinol-cytochrome C reductase 7.2 kda protein (EC 1.10.2.2) | protein | 61 | 77% helix, 0% strand | — |
| N | Mitochondrial ubiquinol-cytochrome-C reductase complex core protein I (EC 1.10.2.2) | protein | 442 | 46% helix, 18% strand | — |
| O | Mitochondrial ubiquinol-cytochrome-C reductase complex core protein 2 (EC 1.10.2.2) | protein | 422 | 41% helix, 19% strand | — |
| P | Cytochrome B (EC 1.10.2.2) | protein | 379 | 69% helix, 2% strand | P18946 |
| T | Mitochondrial ubiquinol-cytochrome C reductase ubiquinone- binding protein qp-C (EC 1.10.2.2) | protein | 79 | 54% helix, 11% strand | — |
| U | Mitochondrial ubiquinol-cytochrome C reductase 11 kda protein, complex III subunit VIII (EC 1.10.2.2) | protein | 67 | 66% helix, 0% strand | — |
| V | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 43 | 7% helix, 12% strand | Q5ZLR5 |
| W | Mitochondrial ubiquinol-cytochrome C reductase 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, F, G, D, E, J, P, S, T, N, Q, R, W
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, P
- 3H1 · 3-chloro-4,6-dihydroxy-2-methyl-5-{(2E,4E)-3-methyl-5-[(1R,2R,6R)-1,2,6-trimethyl-3-oxocyclohexyl]penta-2,4-dien-1-yl}benzaldehyde · ligand · 4 copies · chains C, R, E, 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
- UNL · Unknown ligand · ion · 12 copies · chains A, B, C, E, P, R
- GOL · Glycerol · additive · 2 copies · chains C, D, P, Q
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains C, D, E, J, P, Q, R, W
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 | 551 | 0.87 | 0.93 | 56 | HEM, GOL |
| 2 | 822 | 0.85 | 0.87 | 76 | HEM, UNL, GOL |
| 3 | 716 | 0.84 | 0.88 | 86 | HEM, 3H1 |
| 4 | 417 | 0.81 | 0.89 | 50 | HEM, 3H1 |
| 5 | 118 | 0.80 | 0.99 | 25 | empty |
Interfaces
55 interfaces between chains.
- N–O · 2083 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2056 Ų buried · 31 hydrogen bonds · protein-protein
- O–V · 1748 Ų buried · 18 hydrogen bonds · protein-protein
- B–I · 1675 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1652 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 cofactor (disulfide, heme c attachment).
Compared structures
- 3H1L · Chicken cytochrome BC1 complex with ascochlorin bound at QO and QI sites · the same entry in another collection · chain N against N, 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 3H1L · PDBe 3H1L · UniProt P18946 · UniProt Q5ZLR5
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