MolNFT v1 · #158916 · protein + DNA

Crystal structure of uvrb bound to duplex DNA with ADP

6O8E · Uvrabc system protein B: “Crystal structure of uvrb bound to duplex DNA with ADP”. X-ray diffraction, 4 ligands (ADP, MG, CL), 16 pockets (best druggability 0.80). MolNFT v1 #158916 on GenesisL1: 3D structure, binding sites and…

PDB: 6O8E
Type: protein + DNA
Length: 1,262 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uvrabc system protein B; DNA (5'- D(*GP*CP*TP*CP*TP*AP*GP*AP*TP*TP*TP*TP*CP*AP*TP*AP*CP*GP…
UniProt: P56981
Ligands: ADP, MG, CL, PO4
Pockets: 16 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uvrabc system protein B	protein	592	43% helix, 20% strand	P56981
B	Uvrabc system protein B	protein	590	43% helix, 20% strand	P56981
C, E	DNA (5'- D(GPCPTPCPTPAPGPAPTPTPTPTPCPAPTPAPCPGPGPC)-3')	dna	20	—	—
D, F	DNA (5'- D(GPCPCPGPTPAPTPGPCPCPAPAPTPCPTPAPGPAPGPC)-3')	dna	20	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 4 copies · chains A, B
CL · Chloride ion · ion · 5 copies · chains A, B, F
PO4 · Phosphate ion · ion · 4 copies · chains A, B

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

Pockets

16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	508	0.80	0.87	59	empty
2	923	0.77	0.80	67	empty
3	158	0.74	0.92	28	empty
4	219	0.74	0.89	34	empty
5	962	0.74	0.78	79	empty

Interfaces

7 interfaces between chains.

B–E · 1424 Å² buried · 23 hydrogen bonds · protein-nucleic
A–C · 1389 Å² buried · 24 hydrogen bonds · protein-nucleic
B–F · 912 Å² buried · 8 hydrogen bonds · protein-nucleic
A–D · 888 Å² buried · 6 hydrogen bonds · protein-nucleic
E–F · 810 Å² buried · 77 hydrogen bonds · nucleic-nucleic

Compared structures

6O8E · Crystal structure of UvrB bound to duplex DNA with ADP · the same entry in another collection · chain F against F, TM-score 1.00
P56981 · AlphaFold monomer V2.0 prediction for uvrabc system protein B (P56981) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P56981
Elsewhere: RCSB PDB 6O8E · PDBe 6O8E · UniProt P56981

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