Research workbench
Cryoem structure of the crosslinked RIX7 aaa-ATPase
Analyse Cryoem structure of the crosslinked RIX7 aaa-ATPase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T0V
- Type
- protein
- Length
- 3,397 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RIX7; Polyvaline
- UniProt
- G0RZG1
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RIX7 | protein | 568 | 52% helix, 11% strand | G0RZG1 |
| B | RIX7 | protein | 569 | 51% helix, 11% strand | G0RZG1 |
| C, D | RIX7 | protein | 570 | 50% helix, 11% strand | G0RZG1 |
| E | RIX7 | protein | 540 | 51% helix, 11% strand | G0RZG1 |
| F | RIX7 | protein | 557 | 51% helix, 9% strand | G0RZG1 |
| G | Polyvaline | protein | 23 | 0% helix, 30% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 9 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains E, A, F
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, 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 | 1179 | 0.83 | 0.84 | 103 | ATP, MG |
| 2 | 512 | 0.81 | 0.88 | 63 | ATP, MG |
| 3 | 976 | 0.81 | 0.83 | 115 | empty |
| 4 | 514 | 0.80 | 0.87 | 63 | ATP, MG |
| 5 | 884 | 0.80 | 0.82 | 87 | ATP, MG |
Interfaces
15 interfaces between chains.
- A–B · 4754 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 4603 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 4561 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 4391 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 3127 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7T0V · CryoEM structure of the crosslinked Rix7 AAA-ATPase · 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 G0RZG1
- Elsewhere: RCSB PDB 7T0V · PDBe 7T0V · UniProt G0RZG1
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