Research workbench
Human tom complex without cross-linking
Analyse Human tom complex without cross-linking in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VD2
- Type
- protein
- Length
- 951 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial import receptor subunit TOM6 homolog; Mitochondrial import receptor subunit…
- UniProt
- Q96B49, Q8N4H5, Q9P0U1, Q9NS69, O96008
- Ligands
- PC1
- Pockets
- 19 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 41% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Mitochondrial import receptor subunit TOM6 homolog | protein | 43 | 67% helix, 0% strand | Q96B49 |
| D, E | Mitochondrial import receptor subunit TOM5 homolog | protein | 36 | 94% helix, 0% strand | Q8N4H5 |
| G, J | Mitochondrial import receptor subunit TOM7 homolog | protein | 54 | 69% helix, 0% strand | Q9P0U1 |
| H | Mitochondrial import receptor subunit TOM22 homolog | protein | 56 | 95% helix, 0% strand | Q9NS69 |
| C | Mitochondrial import receptor subunit TOM22 homolog | protein | 57 | 95% helix, 0% strand | Q9NS69 |
| B, I | Mitochondrial import receptor subunit TOM40 homolog | protein | 286 | 3% helix, 66% strand | O96008 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 27 copies · chains A, I, H, F, C, B, G, J, E, D
- UND · Undecane · additive · 16 copies · chains A, F, H, C, B, J, E, I, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.86 | 0.89 | 68 | PC1 |
| 2 | 273 | 0.51 | 0.74 | 30 | PC1 |
| 3 | 238 | 0.50 | 0.74 | 29 | PC1 |
| 4 | 148 | 0.45 | 0.76 | 24 | empty |
| 5 | 178 | 0.44 | 0.74 | 29 | PC1 |
Interfaces
13 interfaces between chains.
- J–B · 1205 Ų buried · 13 hydrogen bonds · protein-protein
- G–I · 1187 Ų buried · 9 hydrogen bonds · protein-protein
- A–I · 956 Ų buried · 3 hydrogen bonds · protein-protein
- F–B · 931 Ų buried · 4 hydrogen bonds · protein-protein
- E–B · 743 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7VD2 · Human TOM complex without cross-linking · the same entry in another collection · chain I against I, TM-score 1.00
- O96008 · AlphaFold monomer V2.0 prediction for mitochondrial import receptor subunit TOM40 homolog… · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q8N4H5 · AlphaFold monomer V2.0 prediction for mitochondrial import receptor subunit TOM5 homolog… · a predicted model of the same protein · chain D against A, TM-score 0.87
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 Q96B49
- Every structure of UniProt Q8N4H5
- Every structure of UniProt Q9P0U1
- Every structure of UniProt Q9NS69
- Every structure of UniProt O96008
- Elsewhere: RCSB PDB 7VD2 · PDBe 7VD2 · UniProt Q96B49 · UniProt Q8N4H5 · UniProt Q9P0U1 · UniProt Q9NS69 · UniProt O96008
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