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Structure of archaeoglobus fulgidis xpb

Analyse Structure of archaeoglobus fulgidis xpb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2FWR
Type: protein
Length: 1,699 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein RAD25
UniProt: O29889
Ligands: PO4
Pockets: 15 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair protein RAD25	protein	434	33% helix, 20% strand	O29889
B	DNA repair protein RAD25	protein	423	34% helix, 22% strand	O29889
C	DNA repair protein RAD25	protein	414	33% helix, 20% strand	O29889
D	DNA repair protein RAD25	protein	428	33% helix, 19% strand	O29889

Ligands and binding sites

PO4 · Phosphate ion · ion · 8 copies · chains A, D, B, C
IPA · Isopropyl alcohol · additive · 3 copies · chains A, D

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

Pockets

15 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	948	0.79	0.81	83	PO4, IPA
2	803	0.78	0.82	82	PO4
3	1057	0.74	0.77	72	empty
4	971	0.72	0.76	82	empty
5	584	0.63	0.74	51	empty

Interfaces

3 interfaces between chains.

A–D · 664 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 656 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 316 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2FWR · Structure of Archaeoglobus Fulgidis XPB · the same entry in another collection · 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 O29889
Elsewhere: RCSB PDB 2FWR · PDBe 2FWR · UniProt O29889

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