MolNFT v1 · #89002 · protein

Hexameric ring of methanococcus voltae rada

4DC9 · DNA repair and recombination protein rada: “Hexameric ring of methanococcus voltae rada”. X-ray diffraction, 1 ligand (NO3), 8 pockets (best druggability 0.78). MolNFT v1 #89002 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4DC9
Type: protein
Length: 1,542 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair and recombination protein rada
UniProt: O73948
Ligands: NO3
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	DNA repair and recombination protein rada	protein	257	35% helix, 27% strand	O73948

Ligands and binding sites

NO3 · Nitrate ion · ion · 12 copies · chains A, B, C, D, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	883	0.78	0.81	81	NO3
2	776	0.78	0.82	77	NO3
3	667	0.77	0.83	64	empty
4	858	0.77	0.81	82	NO3
5	796	0.77	0.81	77	NO3

Interfaces

6 interfaces between chains.

D–E · 1372 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1368 Å² buried · 19 hydrogen bonds · protein-protein
A–F · 1351 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1348 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1346 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4DC9 · Hexameric ring of Methanococcus voltae RadA · the same entry in another collection · chain C against C, TM-score 1.00
O73948 · AlphaFold monomer V2.0 prediction for DNA repair and recombination protein rada (O73948) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 4DC9 · PDBe 4DC9 · UniProt O73948

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