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Crystal structure of E.COLI pol II-abasic DNA binary complex

Analyse Crystal structure of E.COLI pol II-abasic DNA binary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3K5N
Type: protein + DNA
Length: 1,523 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase II; DNA (5'-D(*GP*TP*CP*CP*TP*GP*(3DR)…
EC: 2.7.7.7
UniProt: P21189
Pockets: 18 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase II (EC 2.7.7.7)	protein	759	38% helix, 23% strand	P21189
B	DNA polymerase II (EC 2.7.7.7)	protein	738	41% helix, 24% strand	P21189
T	DNA (5'-D(GPTPCPCPTPGP(3DR) TPAPCPGPCPTPAPGPGPCPAPCPA)-3')	dna	13	—	—
P	DNA (5'-D(GPTPGPCPCPTPAPGPCPGPTPAP*G)-3')	dna	13	—	—

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	380	0.73	0.85	42	empty
2	1112	0.70	0.75	111	empty
3	534	0.69	0.79	73	empty
4	288	0.61	0.79	25	empty
5	289	0.61	0.79	26	empty

Interfaces

4 interfaces between chains.

A–P · 708 Å² buried · 10 hydrogen bonds · protein-nucleic
T–P · 568 Å² buried · 51 hydrogen bonds · nucleic-nucleic
A–B · 455 Å² buried · 5 hydrogen bonds · protein-protein
A–T · 338 Å² buried · 2 hydrogen bonds · protein-nucleic

Compared structures

3K5N · Crystal structure of E.coli Pol II-abasic DNA binary complex · the same entry in another collection · chain A against A, TM-score 1.00
P21189 · AlphaFold monomer V2.0 prediction for DNA polymerase II (P21189) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P21189
Elsewhere: RCSB PDB 3K5N · PDBe 3K5N · UniProt P21189

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