MolNFT v1 · #173457 · protein + DNA

TGOT_6G12 ternary complex

7B0H · DNA (5'-D(P*AP*AP*CP*GP*GP*CP*AP*AP*AP*TP*GP*CP*G)-3'): “TGOT_6G12 ternary complex”. X-ray diffraction, 3 ligands (TTP, MN, MG), 20 pockets (best druggability 0.77). MolNFT v1 #173457 on GenesisL1: 3D structure, binding sites and…

PDB: 7B0H
Type: protein + DNA
Length: 1,513 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(P*AP*AP*CP*GP*GP*CP*AP*AP*AP*TP*GP*CP*G)-3'); DNA…
EC: 2.7.7.7
UniProt: P56689
Ligands: TTP, MN, MG
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	DNA (5'-D(PAPAPCPGPGPCPAPAPAPTPGPCP*G)-3')	dna	13	—	—
D, G	DNA (5'-D(PCPGPCPAPTPT)-3')	dna	6	—	—
E	DNA polymerase (EC 2.7.7.7)	protein	713	41% helix, 23% strand	P56689
F	DNA polymerase (EC 2.7.7.7)	protein	762	41% helix, 23% strand	P56689

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, E, G, C, D, F
MN · Manganese (II) ion · metal · 4 copies · chains E, F
MG · Magnesium ion · metal · 2 copies · chains E, G, D, F

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	676	0.77	0.83	58	empty
2	613	0.75	0.82	63	MN, MG, TTP
3	259	0.70	0.85	40	MN, TTP
4	98	0.69	0.93	22	empty
5	131	0.67	0.89	22	empty

Interfaces

9 interfaces between chains.

C–F · 1561 Å² buried · 27 hydrogen bonds · protein-nucleic
A–E · 1467 Å² buried · 29 hydrogen bonds · protein-nucleic
E–F · 589 Å² buried · 3 hydrogen bonds · protein-protein
A–F · 398 Å² buried · 10 hydrogen bonds · protein-nucleic
D–F · 368 Å² buried · 9 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7B0H · TgoT_6G12 Ternary complex · the same entry in another collection · chain G against G, TM-score 1.00
P56689 · AlphaFold monomer V2.0 prediction for DNA polymerase (P56689) · a predicted model of the same protein · chain E 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 P56689
Elsewhere: RCSB PDB 7B0H · PDBe 7B0H · UniProt P56689

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