MolNFT v1 · #173455 · protein + DNA

TGOT_6G12 binary complex

7B0F · DNA polymerase: “TGOT_6G12 binary complex”. X-ray diffraction, 1 ligand (TTP), 11 pockets (best druggability 0.74). MolNFT v1 #173455 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7B0F
Type: protein + DNA
Length: 740 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase; DNA (5'-D(P*CP*GP*CP*AP*TP*T)-3'); DNA…
EC: 2.7.7.7
UniProt: P56689
Ligands: TTP
Pockets: 11 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase (EC 2.7.7.7)	protein	721	42% helix, 22% strand	P56689
B	DNA (5'-D(PCPGPCPAPTPT)-3')	dna	6	—	—
C	DNA (5'-D(PAPAPCPGPGPCPTPAPAPTPGPCP*G)-3')	dna	13	—	—

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	110	0.74	0.95	21	empty
2	93	0.59	0.88	18	empty
3	269	0.58	0.78	32	empty
4	274	0.58	0.78	31	empty
5	260	0.58	0.78	30	empty

Interfaces

3 interfaces between chains.

A–C · 1590 Å² buried · 29 hydrogen bonds · protein-nucleic
A–B · 405 Å² buried · 7 hydrogen bonds · protein-nucleic
B–C · 273 Å² buried · 24 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7B0F · TgoT_6G12 Binary complex · 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 0.95

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 P56689
Elsewhere: RCSB PDB 7B0F · PDBe 7B0F · UniProt P56689

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