MolNFT v1 · #161562 · protein
Truncated human R2TP complex, structure 4 (ADP-empty)
6QI9 · Ruvb-like 1: “Truncated human R2TP complex, structure 4 (ADP-empty)”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.87). MolNFT v1 #161562 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6QI9
- Type
- protein
- Length
- 1,879 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 0.87
Structure
electron microscopy · 6 distinct chains · 43% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ruvb-like 1 (EC 3.6.4.12) | protein | 317 | 47% helix, 9% strand | Q9Y265 |
| B | Ruvb-like 1 (EC 3.6.4.12) | protein | 310 | 40% helix, 13% strand | Q9Y265 |
| C | Ruvb-like 1 (EC 3.6.4.12) | protein | 316 | 40% helix, 13% strand | Q9Y265 |
| D | Ruvb-like 2 (EC 3.6.4.12) | protein | 268 | 47% helix, 10% strand | Q9Y230 |
| E | Ruvb-like 2 (EC 3.6.4.12) | protein | 335 | 42% helix, 11% strand | Q9Y230 |
| F | Ruvb-like 2 (EC 3.6.4.12) | protein | 333 | 43% helix, 11% strand | Q9Y230 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, 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 | 1036 | 0.87 | 0.88 | 105 | ADP |
| 2 | 912 | 0.86 | 0.88 | 101 | ADP |
| 3 | 1104 | 0.85 | 0.85 | 110 | ADP |
| 4 | 729 | 0.83 | 0.87 | 59 | ADP |
| 5 | 1175 | 0.83 | 0.84 | 111 | ADP |
Interfaces
6 interfaces between chains.
- B–E · 2685 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 2461 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 1963 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 1901 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1768 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
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 6QI9 · PDBe 6QI9 · UniProt Q9Y265 · UniProt Q9Y230
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