Research workbench
Plant mitochondrial complex III2 from vigna radiata
Analyse Plant mitochondrial complex III2 from vigna radiata in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JRG
- Type
- protein
- Length
- 3,983 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1; Alpha-mpp…
- EC
- 7.1.1.8
- UniProt
- A0A1S3TWG4, A0A1S3VF71, A0A1S3W199, A0A1S3TB49, A0A1S3U9J1, A0A1S3U9S5, A0A1S3VHC0, A0A1S3TQD2
- Ligands
- 3PE, CDL, HEM, PC1, HEC, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 16 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M | Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1 | protein | 487 | 44% helix, 16% strand | A0A1S3TWG4 |
| B | Alpha-mpp | protein | 457 | 42% helix, 19% strand | A0A1S3VF71 |
| C, O | Cob | protein | 388 | 67% helix, 2% strand | — |
| D, P | Cytochrome C1-2, heme protein, mitochondrial | protein | 244 | 41% helix, 9% strand | A0A1S3W199 |
| E | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 7.1.1.8) | protein | 77 | 55% helix, 3% strand | A0A1S3TB49 |
| F | Cytochrome B-C1 complex subunit 7 | protein | 116 | 64% helix, 0% strand | A0A1S3U9J1 |
| G, S | Cytochrome B-C1 complex subunit 8 | protein | 70 | 61% helix, 9% strand | A0A1S3U9S5 |
| H | Cytochrome B-C1 complex subunit 6 | protein | 65 | 78% helix, 0% strand | A0A1S3VHC0 |
| J | Cytochrome B-C1 complex subunit 9 | protein | 60 | 72% helix, 0% strand | A0A1S3TQD2 |
| K | QCR10 | protein | 31 | 71% helix, 0% strand | — |
| N | Alpha-mpp | protein | 455 | 43% helix, 17% strand | A0A1S3VF71 |
| Q | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 7.1.1.8) | protein | 74 | 51% helix, 3% strand | A0A1S3TB49 |
| R | Cytochrome B-C1 complex subunit 7 | protein | 115 | 63% helix, 0% strand | A0A1S3U9J1 |
| T | Cytochrome B-C1 complex subunit 6 | protein | 64 | 78% helix, 0% strand | A0A1S3VHC0 |
| V | Cytochrome B-C1 complex subunit 9 | protein | 59 | 66% helix, 0% strand | A0A1S3TQD2 |
| W | QCR10 | protein | 32 | 81% helix, 0% strand | — |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 17 copies · chains C, O, R, F, G, D, E, J, M, V, W, K, P, S, Q
- CDL · Cardiolipin · ligand · 9 copies · chains A, C, J, K, D, E, F, G, M, O, V, W, P, Q, R, S
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, O
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 3 copies · chains A, E, J, K, M, Q, V, W, P, S
- HEC · Heme C · ligand · 2 copies · chains D, P
- ZN · Zinc ion · metal · 2 copies · chains A, M
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 | 741 | 0.85 | 0.88 | 71 | HEM |
| 2 | 807 | 0.84 | 0.86 | 83 | HEM |
| 3 | 762 | 0.84 | 0.87 | 70 | HEM |
| 4 | 730 | 0.83 | 0.87 | 70 | HEM |
| 5 | 902 | 0.83 | 0.84 | 77 | empty |
Interfaces
62 interfaces between chains.
- M–N · 3907 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 3790 Ų buried · 41 hydrogen bonds · protein-protein
- O–R · 1948 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1871 Ų buried · 13 hydrogen bonds · protein-protein
- O–P · 1695 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 cofactor (disulfide, heme c attachment).
Compared structures
- 7JRG · Plant Mitochondrial complex III2 from Vigna radiata · 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 A0A1S3TWG4
- Every structure of UniProt A0A1S3VF71
- Every structure of UniProt A0A1S3W199
- Every structure of UniProt A0A1S3TB49
- Every structure of UniProt A0A1S3U9J1
- Every structure of UniProt A0A1S3U9S5
- Every structure of UniProt A0A1S3VHC0
- Every structure of UniProt A0A1S3TQD2
- Elsewhere: RCSB PDB 7JRG · PDBe 7JRG · UniProt A0A1S3TWG4 · UniProt A0A1S3VF71 · UniProt A0A1S3W199 · UniProt A0A1S3TB49 · UniProt A0A1S3U9J1 · UniProt A0A1S3U9S5 · UniProt A0A1S3VHC0 · UniProt A0A1S3TQD2
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