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Crystal structure of DNA polymerase complexed with DNA and cr-pcp

Analyse Crystal structure of DNA polymerase complexed with DNA and cr-pcp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1HUZ
Type: protein + DNA
Length: 682 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*AP*TP*AP*GP*GP*CP*GP*TP*CP*G)-3'; 5'-D(P*CP*GP*AP*CP*GP*CP*CP*T)-3'; DNA…
EC: 2.7.7.7
UniProt: P06766
Ligands: MDN, CR
Pockets: 4 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T, C	5'-D(APAPTPAPGPGPCPGPTPCP*G)-3'	dna	8	—	—
P, D	5'-D(PCPGPAPCPGPCPCPT)-3'	dna	8	—	—
A, B	DNA polymerase beta (EC 2.7.7.7)	protein	325	47% helix, 13% strand	P06766

Ligands and binding sites

MDN · Methylenediphosphonic acid · ligand · 2 copies · chains P, A, D, B
CR · Chromium ion · metal · 2 copies · chains P, A, D, 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	236	0.60	0.81	25	empty
2	455	0.59	0.75	41	CR, MDN
3	219	0.57	0.80	23	empty
4	451	0.57	0.74	42	CR, MDN

Interfaces

6 interfaces between chains.

C–B · 637 Å² buried · 16 hydrogen bonds · protein-nucleic
T–A · 619 Å² buried · 12 hydrogen bonds · protein-nucleic
D–B · 535 Å² buried · 17 hydrogen bonds · protein-nucleic
P–A · 533 Å² buried · 14 hydrogen bonds · protein-nucleic
C–D · 372 Å² buried · 33 hydrogen bonds · nucleic-nucleic

Compared structures

1HUZ · Crystal structure of DNA polymerase complexed with DNA and cr-pcp · the same entry in another collection · chain B against B, TM-score 1.00
P06766 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06766) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P06766
Elsewhere: RCSB PDB 1HUZ · PDBe 1HUZ · UniProt P06766

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