MolNFT v1 · #65597 · protein
Chicken cytochrome BC1 complex with ascochlorin bound at qo and qi sites
3H1L · Mitochondrial ubiquinol-cytochrome-C reductase complex core…: “Chicken cytochrome BC1 complex with ascochlorin bound at qo and qi sites”. X-ray diffraction, 7 ligands (PEE, HEM, 3H1), 20 pockets (best druggability 0.87). MolNFT v1…
- 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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