MolNFT v1 · #170015 · protein

HUMRADA33F in complex with peptidic inhibitor 6

6XTW · DNA repair and recombination protein rada: “HUMRADA33F in complex with peptidic inhibitor 6”. X-ray diffraction, 2 ligands (NZW, SO4), 4 pockets (best druggability 0.61). MolNFT v1 #170015 on GenesisL1: 3D structure, binding sites…

PDB: 6XTW
Type: protein
Length: 453 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair and recombination protein rada
UniProt: O74036
Ligands: NZW, SO4
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair and recombination protein rada	protein	225	38% helix, 26% strand	O74036
B	DNA repair and recombination protein rada	protein	228	37% helix, 26% strand	O74036

Ligands and binding sites

NZW · ~{N}-[2-[(2~{S})-2-[[(1~{S})-1-(4-methoxyphenyl) ethyl]carbamoyl]pyrrolidin-1-yl]-2-oxidanylidene-ethyl]quinoline-2-carboxamide · ligand · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	200	0.61	0.82	41	empty
2	248	0.55	0.77	37	empty
3	77	0.39	0.78	19	SO4
4	52	0.33	0.78	17	SO4

Interfaces

1 interface between chains.

A–B · 929 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6XTW · HumRadA33F in complex with peptidic inhibitor 6 · the same entry in another collection · chain A against A, TM-score 1.00
O74036 · AlphaFold monomer V2.0 prediction for DNA repair and recombination protein rada (O74036) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 O74036
Elsewhere: RCSB PDB 6XTW · PDBe 6XTW · UniProt O74036

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