Research workbench
RUVBL1-RUVBL2 with truncated domain II in complex with phosphorylated cordycepin
Analyse RUVBL1-RUVBL2 with truncated domain II in complex with phosphorylated cordycepin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K0R
- Type
- protein
- Length
- 3,705 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ruvb-like 1,RUVB-like 1; Ruvb-like 2,RUVB-like 2
- EC
- 3.6.4.12
- UniProt
- Q9Y265, Q9Y230
- Ligands
- CUU, 3AT, ADP, CU0, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 11 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ruvb-like 1,RUVB-like 1 (EC 3.6.4.12) | protein | 316 | 49% helix, 17% strand | Q9Y265 |
| B, H | Ruvb-like 1,RUVB-like 1 (EC 3.6.4.12) | protein | 318 | 47% helix, 17% strand | Q9Y265 |
| C | Ruvb-like 1,RUVB-like 1 (EC 3.6.4.12) | protein | 313 | 48% helix, 18% strand | Q9Y265 |
| D | Ruvb-like 2,RUVB-like 2 (EC 3.6.4.12) | protein | 303 | 47% helix, 18% strand | Q9Y230 |
| E | Ruvb-like 2,RUVB-like 2 (EC 3.6.4.12) | protein | 304 | 49% helix, 17% strand | Q9Y230 |
| F | Ruvb-like 2,RUVB-like 2 (EC 3.6.4.12) | protein | 307 | 50% helix, 18% strand | Q9Y230 |
| G | Ruvb-like 1,RUVB-like 1 (EC 3.6.4.12) | protein | 311 | 48% helix, 17% strand | Q9Y265 |
| I | Ruvb-like 1,RUVB-like 1 (EC 3.6.4.12) | protein | 313 | 49% helix, 17% strand | Q9Y265 |
| J | Ruvb-like 2,RUVB-like 2 (EC 3.6.4.12) | protein | 302 | 48% helix, 17% strand | Q9Y230 |
| K | Ruvb-like 2,RUVB-like 2 (EC 3.6.4.12) | protein | 300 | 48% helix, 18% strand | Q9Y230 |
| L | Ruvb-like 2,RUVB-like 2 (EC 3.6.4.12) | protein | 300 | 47% helix, 16% strand | Q9Y230 |
Ligands and binding sites
- CUU · [(2~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate · ligand · 8 copies · chains B, C, D, F, G, H, I, K
- 3AT · 3'-deoxyadenosine-5'-triphosphate · ligand · 2 copies · chains A, E, I, J
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- CU0 · [(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate · ligand · chains L
- MG · Magnesium ion · metal · 2 copies · chains C, D, H, L
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 | 968 | 0.85 | 0.86 | 106 | CUU |
| 2 | 1127 | 0.85 | 0.85 | 115 | CUU |
| 3 | 1126 | 0.84 | 0.85 | 119 | ADP |
| 4 | 1077 | 0.83 | 0.84 | 102 | CUU |
| 5 | 1146 | 0.83 | 0.84 | 119 | CUU |
Interfaces
14 interfaces between chains.
- B–D · 2075 Ų buried · 18 hydrogen bonds · protein-protein
- G–L · 1917 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 1912 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1909 Ų buried · 17 hydrogen bonds · protein-protein
- I–K · 1882 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6K0R · Ruvbl1-Ruvbl2 with truncated domain II in complex with phosphorylated Cordycepin · the same entry in another collection · chain L against L, 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 Q9Y265
- Every structure of UniProt Q9Y230
- Elsewhere: RCSB PDB 6K0R · PDBe 6K0R · UniProt Q9Y265 · UniProt Q9Y230
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.