MolNFT v1 · #91640 · protein + DNA

RB69 DNA polymerase ternary complex with DTTP/DT

4FJ9: “RB69 DNA polymerase ternary complex with DTTP/DT”. X-ray diffraction, 2 ligands (TTP, CA), 10 pockets (best druggability 0.84). MolNFT v1 #91640 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4FJ9
Type: protein + DNA
Length: 931 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase; DNA template; DNA primer
EC: 2.7.7.7
UniProt: Q38087
Ligands: TTP, CA
Pockets: 10 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase (EC 2.7.7.7)	protein	901	45% helix, 19% strand	Q38087
T	DNA template	dna	17	—	—
P	DNA primer	dna	13	—	—

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · chains A, T, P
CA · Calcium ion · metal · 5 copies · chains A, P

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	279	0.84	0.95	33	empty
2	443	0.76	0.85	63	TTP, CA
3	416	0.75	0.84	37	CA
4	199	0.61	0.82	25	empty
5	391	0.60	0.76	45	empty

Interfaces

3 interfaces between chains.

A–T · 1219 Å² buried · 22 hydrogen bonds · protein-nucleic
A–P · 711 Å² buried · 17 hydrogen bonds · protein-nucleic
T–P · 598 Å² buried · 55 hydrogen bonds · nucleic-nucleic

Compared structures

4FJ9 · RB69 DNA polymerase ternary complex with dTTP/dT · the same entry in another collection · chain A against A, TM-score 1.00

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 Q38087
Elsewhere: RCSB PDB 4FJ9 · PDBe 4FJ9 · UniProt Q38087

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