Research workbench

DNA polymerase I klenow fragment (E.C.2.7.7.7) MUTANT/DNA complex

Analyse DNA polymerase I klenow fragment (E.C.2.7.7.7) MUTANT/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KLN
Type: protein + DNA
Length: 618 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*CP*CP*TP*CP*GP*CP*GP*GP*CP*GP*GP*C)-3'); DNA…
UniProt: P00582
Ligands: ZN
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA (5'-D(GPCPCPTPCPGPCPGPGPCPGPGP*C)-3')	dna	13	—	—
C	DNA (5'-D(GPCPCPGPCPGPAPGPGPC)-3')	dna	10	—	—
A	Protein (DNA polymerase I klenow fragment (E.C.2.7.7.7))	protein	595	52% helix, 14% strand	P00582

Ligands and binding sites

ZN · Zinc ion · metal · chains B, A

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

Pockets

8 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	700	0.75	0.81	66	empty
2	56	0.60	0.92	20	ZN
3	290	0.59	0.78	41	empty
4	160	0.52	0.79	25	empty
5	162	0.47	0.77	26	empty

Interfaces

3 interfaces between chains.

B–A · 1034 Å² buried · 24 hydrogen bonds · protein-nucleic
B–C · 464 Å² buried · 52 hydrogen bonds · nucleic-nucleic
C–A · 268 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

1KLN · DNA polymerase I klenow fragment (E.C.2.7.7.7) MUTANT/DNA complex · the same entry in another collection · chain B against B, TM-score 1.00
P00582 · AlphaFold monomer V2.0 prediction for DNA polymerase I (P00582) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P00582
Elsewhere: RCSB PDB 1KLN · PDBe 1KLN · UniProt P00582

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