Research workbench
Human RVB1/RVB2 heterohexamer in INO80 complex
Analyse Human RVB1/RVB2 heterohexamer in INO80 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OAF
- Type
- protein
- Length
- 2,538 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ruvb-like 1; Ruvb-like 2
- EC
- 3.6.4.12
- UniProt
- Q9Y265, Q9Y230
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ruvb-like 1 (EC 3.6.4.12) | protein | 436 | 38% helix, 21% strand | Q9Y265 |
| B | Ruvb-like 2 (EC 3.6.4.12) | protein | 418 | 38% helix, 17% strand | Q9Y230 |
| C | Ruvb-like 1 (EC 3.6.4.12) | protein | 424 | 39% helix, 22% strand | Q9Y265 |
| D | Ruvb-like 2 (EC 3.6.4.12) | protein | 411 | 41% helix, 18% strand | Q9Y230 |
| E | Ruvb-like 1 (EC 3.6.4.12) | protein | 442 | 37% helix, 18% strand | Q9Y265 |
| F | Ruvb-like 2 (EC 3.6.4.12) | protein | 407 | 36% helix, 19% strand | Q9Y230 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
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 | 611 | 0.85 | 0.90 | 73 | ADP |
| 2 | 359 | 0.84 | 0.93 | 49 | ADP |
| 3 | 1085 | 0.84 | 0.85 | 111 | empty |
| 4 | 1019 | 0.83 | 0.84 | 118 | empty |
| 5 | 1050 | 0.83 | 0.84 | 85 | empty |
Interfaces
12 interfaces between chains.
- A–B · 3672 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 3623 Ų buried · 28 hydrogen bonds · protein-protein
- A–F · 3563 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 3377 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 3335 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5OAF · Human Rvb1/Rvb2 heterohexamer in INO80 complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q9Y230 · AlphaFold monomer V2.0 prediction for ruvb-like 2 (Q9Y230) · a predicted model of the same protein · chain B against A, TM-score 0.83
- Q9Y265 · AlphaFold monomer V2.0 prediction for ruvb-like 1 (Q9Y265) · a predicted model of the same protein · chain A 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 Q9Y265
- Every structure of UniProt Q9Y230
- Elsewhere: RCSB PDB 5OAF · PDBe 5OAF · UniProt Q9Y265 · UniProt Q9Y230
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