Research workbench
Full-length human mitochondrial HSP90 (TRAP1) in complex with sdhb in the presence of AMP-pnp
Analyse Full-length human mitochondrial HSP90 (TRAP1) in complex with sdhb in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KCM
- Type
- protein
- Length
- 1,347 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock protein 75 kda, mitochondrial; Succinate dehydrogenase [ubiquinone]…
- UniProt
- Q12931, P21912
- Ligands
- ANP, FES, MG, K
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heat shock protein 75 kda, mitochondrial | protein | 612 | 39% helix, 19% strand | Q12931 |
| B | Heat shock protein 75 kda, mitochondrial | protein | 614 | 41% helix, 19% strand | Q12931 |
| C | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial | protein | 121 | 21% helix, 25% strand | P21912 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · chains C
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.86 | 0.87 | 86 | empty |
| 2 | 264 | 0.79 | 0.91 | 42 | ANP, MG, K |
| 3 | 727 | 0.79 | 0.83 | 62 | empty |
| 4 | 286 | 0.78 | 0.90 | 44 | ANP, MG, K |
| 5 | 168 | 0.61 | 0.83 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5654 Ų buried · 62 hydrogen bonds · protein-protein
- B–C · 987 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 939 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7KCM · Full-length human mitochondrial Hsp90 (TRAP1) in complex with SdhB in the presence of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12931 · AlphaFold monomer V2.0 prediction for heat shock protein 75 kda, mitochondrial (Q12931) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P21912 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] iron-sulfur… · a predicted model of the same protein · chain C against A, TM-score 0.79
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 Q12931
- Every structure of UniProt P21912
- Elsewhere: RCSB PDB 7KCM · PDBe 7KCM · UniProt Q12931 · UniProt P21912
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