Research workbench
Cytochrome BC1 bound to the inhibitor MJM170
Analyse Cytochrome BC1 bound to the inhibitor MJM170 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NMI
- Type
- protein
- Length
- 3,934 residues
- Chains
- 22
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B-C1 complex subunit 1, mitochondrial; Cytochrome B-C1 complex subunit 2…
- EC
- 1.10.2.2
- UniProt
- P31800, P23004, P00157, P00125, P13272, P00129, P13271, P00126, P00130
- Ligands
- PEE, CDL, HEM, MJM, HEC, FES
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 15 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 444 | 47% helix, 19% strand | P31800 |
| B, O | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 423 | 43% helix, 18% strand | P23004 |
| C, P | Cytochrome B | protein | 372 | 73% helix, 2% strand | P00157 |
| D, Q | Cytochrome C1, heme protein, mitochondrial | protein | 240 | 42% helix, 8% strand | P00125 |
| E | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 196 | 32% helix, 17% strand | P13272 |
| F, S | Cytochrome B-C1 complex subunit 7 | protein | 99 | 70% helix, 1% strand | P00129 |
| G | Cytochrome B-C1 complex subunit 8 | protein | 74 | 57% helix, 12% strand | P13271 |
| H | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 66 | 70% helix, 0% strand | P00126 |
| I, V | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 30 | 13% helix, 27% strand | P13272 |
| J | Cytochrome B-C1 complex subunit 9 | protein | 59 | 68% helix, 0% strand | P00130 |
| K, X | Arg-asn-TRP-val-pro-thr-ala-gln-leu-TRP-gly-ala-val-gly- ala-val-gly-leu-val-ser-ala-thr | protein | 22 | 86% helix, 0% strand | — |
| R | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 72 | 67% helix, 1% strand | P13272 |
| T | Cytochrome B-C1 complex subunit 8 | protein | 80 | 53% helix, 11% strand | P13271 |
| U | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 68 | 68% helix, 0% strand | P00126 |
| W | Cytochrome B-C1 complex subunit 9 | protein | 59 | 68% helix, 0% strand | P00130 |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 6 copies · chains C, F, G, D, E, J, A, P, S, T, Q, R, W, N
- CDL · Cardiolipin · ligand · 6 copies · chains A, C, F, G, D, P, Q, T, N, S
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, P
- MJM · (4aS)-2-methyl-3-(4-phenoxyphenyl)-5,6,7,8-tetrahydroquinolin-4(4aH)-one · ligand · 2 copies · chains C, P
- HEC · Heme C · ligand · 2 copies · chains D, Q
- FES · Fe2/s2 (inorganic) cluster · ligand · chains E
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 | 362 | 0.85 | 0.94 | 42 | HEM |
| 2 | 607 | 0.83 | 0.88 | 68 | HEM |
| 3 | 997 | 0.83 | 0.83 | 94 | CDL, PEE |
| 4 | 1072 | 0.82 | 0.83 | 94 | PEE, CDL |
| 5 | 838 | 0.82 | 0.84 | 88 | empty |
Interfaces
60 interfaces between chains.
- N–O · 2373 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2344 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1747 Ų buried · 20 hydrogen bonds · protein-protein
- P–Q · 1735 Ų buried · 18 hydrogen bonds · protein-protein
- O–V · 1558 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 cofactor (disulfide, heme c attachment).
Compared structures
- 5NMI · Cytochrome bc1 bound to the inhibitor MJM170 · the same entry in another collection · chain K against K, 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 P31800
- Every structure of UniProt P23004
- Every structure of UniProt P00157
- Every structure of UniProt P00125
- Every structure of UniProt P13272
- Every structure of UniProt P00129
- Every structure of UniProt P13271
- Every structure of UniProt P00126
- Every structure of UniProt P00130
- Elsewhere: RCSB PDB 5NMI · PDBe 5NMI · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130
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