MolNFT v1 · #104772 · protein
Rada from methanococcus voltae in complex with copper phthalocyanine tetrasulfonate inhibitor
4QKQ · DNA repair and recombination protein rada: “Rada from methanococcus voltae in complex with copper phthalocyanine tetrasulfonate inhibitor”. X-ray diffraction, 2 ligands (35N, NO3), 20 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 4QKQ
- Type
- protein
- Length
- 3,084 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair and recombination protein rada
- UniProt
- O73948
- Ligands
- 35N, NO3
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | DNA repair and recombination protein rada | protein | 257 | 39% helix, 26% strand | O73948 |
Ligands and binding sites
- 35N · Copper(II) tetrapyrrole · ligand
- NO3 · Nitrate ion · ion · 30 copies · chains A, J, B, C, H, D, G, E, L, F, K, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.78 | 0.81 | 87 | NO3 |
| 2 | 991 | 0.78 | 0.80 | 93 | NO3 |
| 3 | 950 | 0.78 | 0.80 | 83 | NO3 |
| 4 | 857 | 0.78 | 0.81 | 77 | NO3 |
| 5 | 889 | 0.78 | 0.81 | 87 | NO3 |
Interfaces
18 interfaces between chains.
- A–B · 1280 Ų buried · 11 hydrogen bonds · protein-protein
- G–L · 1279 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 1278 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 1275 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1274 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4QKQ · RadA from Methanococcus Voltae in complex with copper phthalocyanine tetrasulfonate… · 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 O73948
- Elsewhere: RCSB PDB 4QKQ · PDBe 4QKQ · UniProt O73948
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