Research workbench

Klenow fragment with bridging-sulfur substrate and zinc only

Analyse Klenow fragment with bridging-sulfur substrate and zinc only in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2KFZ
Type: protein + DNA
Length: 604 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*CP*TP*TP*AP*(US1)P*G)-3'; Klenow fragment of DNA polymerase I
EC: 2.7.7.7
UniProt: P00582
Ligands: ZN, MG
Pockets: 7 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	5'-D(GPCPTPTPAP(US1)P*G)-3'	dna	3	—	—
A	Klenow fragment of DNA polymerase I (EC 2.7.7.7)	protein	601	51% helix, 13% strand	P00582

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains B, A
MG · Magnesium ion · metal · chains A

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	152	0.54	0.81	21	empty
2	302	0.50	0.73	43	ZN
3	66	0.43	0.82	19	empty
4	100	0.38	0.76	18	empty
5	96	0.37	0.75	18	empty

Interfaces

1 interface between chains.

B–A · 657 Å² buried · 17 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

2KFZ · Klenow fragment with bridging-sulfur substrate and zinc only · 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 0.95

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 P00582
Elsewhere: RCSB PDB 2KFZ · PDBe 2KFZ · UniProt P00582

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