MolNFT v1 · #131622 · protein

Pandda analysis group deposition -- crystal structure of DCLRE1A after initial refinement with no ligand modelled (structure 284)

5QA2 · DNA cross-link repair 1A protein: “Pandda analysis group deposition -- crystal structure of DCLRE1A after initial refinement with no ligand…”. X-ray diffraction, 1 ligand (NI), 5 pockets (best druggability 0.57). MolNFT v1 #131622…

PDB: 5QA2
Type: protein
Length: 341 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA cross-link repair 1A protein
UniProt: Q6PJP8
Ligands: NI
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA cross-link repair 1A protein	protein	341	35% helix, 22% strand	Q6PJP8

Ligands and binding sites

NI · Nickel (II) ion · metal · chains A
MLI · Malonate ion · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	231	0.57	0.79	37	MLI
2	111	0.36	0.73	24	empty
3	59	0.35	0.78	16	empty
4	74	0.32	0.74	17	empty
5	51	0.27	0.74	14	empty

Compared structures

Q6PJP8 · AlphaFold monomer V2.0 prediction for DNA cross-link repair 1A protein (Q6PJP8) · a predicted model of the same protein · chain A against A, 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 Q6PJP8
Elsewhere: RCSB PDB 5QA2 · PDBe 5QA2 · UniProt Q6PJP8

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