MolNFT v1 · #152764 · protein + DNA

Structure of 9N-I DNA polymerase incorporation with dg in the active site

6ISG: “Structure of 9N-I DNA polymerase incorporation with dg in the active site”. X-ray diffraction, 2 ligands (PPV, CA), 10 pockets (best druggability 0.77). MolNFT v1 #152764 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ISG
Type: protein + DNA
Length: 785 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase; DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*G)- 3'); DNA…
EC: 2.7.7.7
UniProt: Q56366
Ligands: PPV, CA
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase (EC 2.7.7.7)	protein	754	42% helix, 21% strand	Q56366
C	DNA (5'-D(GPCPGPGPAPCPTPGPCPTPTPAPCPCP*G)- 3')	dna	15	—	—
D	DNA (5'-D(GPAPCPGPGPTPAPAPGPCPAPGPTPCPCPG)- 3')	dna	16	—	—

Ligands and binding sites

PPV · Pyrophosphate · ligand · chains A
CA · Calcium ion · metal · 5 copies · chains A, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	300	0.77	0.89	41	empty
2	165	0.74	0.92	40	empty
3	576	0.69	0.78	54	empty
4	348	0.69	0.82	63	empty
5	327	0.66	0.81	40	empty

Interfaces

3 interfaces between chains.

A–D · 933 Å² buried · 13 hydrogen bonds · protein-nucleic
A–C · 698 Å² buried · 14 hydrogen bonds · protein-nucleic
C–D · 637 Å² buried · 44 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6ISG · Structure of 9N-I DNA polymerase incorporation with dG in the active site · the same entry in another collection · chain A against A, TM-score 1.00
Q56366 · AlphaFold monomer V2.0 prediction for DNA polymerase (Q56366) · 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 Q56366
Elsewhere: RCSB PDB 6ISG · PDBe 6ISG · UniProt Q56366

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