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Kod polymerase in binary complex with dsdna

Analyse Kod polymerase in binary complex with dsdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4K8Z
Type: protein + DNA
Length: 782 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase; DNA (5'-D(*AP*AP*AP*TP*TP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)- 3'); DNA…
EC: 2.7.7.7
UniProt: P77933
Ligands: NCO, MG
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase (EC 2.7.7.7)	protein	756	42% helix, 23% strand	P77933
T	DNA (5'-D(APAPAPTPTPCPGPCPAPGPTPTPCPGPCPG)- 3')	dna	14	—	—
P	DNA (5'-D(CPGPCPGPAPAPCPTPGPCPGP(2DA))-3')	dna	12	—	—

Ligands and binding sites

NCO · Cobalt hexammine(iii) · ligand · chains A
MG · Magnesium ion · metal · chains T
EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1102	0.77	0.79	71	EDO
2	183	0.75	0.92	32	empty
3	994	0.72	0.76	73	empty
4	391	0.62	0.77	51	empty
5	226	0.56	0.78	22	empty

Interfaces

3 interfaces between chains.

A–T · 1131 Å² buried · 18 hydrogen bonds · protein-nucleic
A–P · 749 Å² buried · 23 hydrogen bonds · protein-nucleic
T–P · 567 Å² buried · 49 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

4K8Z · KOD Polymerase in binary complex with dsDNA · the same entry in another collection · chain P against P, TM-score 1.00
P77933 · AlphaFold monomer V2.0 prediction for DNA polymerase (P77933) · 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 P77933
Elsewhere: RCSB PDB 4K8Z · PDBe 4K8Z · UniProt P77933

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