MolNFT v1 · #173447 · protein

TGOT_6G12 apo

7B07 · DNA polymerase: “TGOT_6G12 apo”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.65). MolNFT v1 #173447 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7B07
Type: protein
Length: 749 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase
EC: 2.7.7.7
UniProt: P56689
Ligands: CA
Pockets: 9 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase (EC 2.7.7.7)	protein	749	43% helix, 22% strand	P56689

Ligands and binding sites

CA · Calcium ion · metal · 4 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.65	0.94	16	empty
2	448	0.63	0.77	49	empty
3	219	0.56	0.78	24	empty
4	243	0.52	0.76	35	CA
5	121	0.50	0.80	21	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7B07 · TgoT_6G12 apo · the same entry in another collection · chain A against A, TM-score 1.00
P56689 · AlphaFold monomer V2.0 prediction for DNA polymerase (P56689) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 P56689
Elsewhere: RCSB PDB 7B07 · PDBe 7B07 · UniProt P56689

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