MolNFT v1 · #157282 · protein + DNA

Bst DNA polymerase I TNA/DNA binary complex

6MU5 · DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'): “Bst DNA polymerase I TNA/DNA binary complex”. X-ray diffraction, 5 ligands (TG, TFT, FA2), 7 pockets (best druggability 0.68). MolNFT v1 #157282 on GenesisL1: 3D structure, binding…

PDB: 6MU5
Type: protein + DNA
Length: 588 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'); DNA polymerase I
EC: 2.7.7.7
UniProt: E1C9K5
Ligands: TG, TFT, FA2, TC, SO4
Pockets: 7 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 55% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	DNA (5'-D(PGPCPGPAPTPCPAPCPGPT)-3')	dna	10	—	—
A	DNA polymerase I (EC 2.7.7.7)	protein	578	55% helix, 13% strand	E1C9K5

Ligands and binding sites

TG · 2-azanyl-9-[(2~{R},3~{R},4~{S})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-oxolan-2-yl]-1~{H}-purin-6-one · ligand · 4 copies · chains A, P
TFT · (L)-alpha-threofuranosyl-thymine-3'-monophosphate · ligand · 3 copies · chains A, P
FA2 · 5-(6-amino-9H-purin-9-yl)-4-hydroxytetrahydrofuran-3-yl dihydrogen phosphate · ligand · 3 copies · chains P, A
TC · 4-azanyl-1-[(2~{R},3~{R},4~{S})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$L^{6}-phosphanyl]oxy-oxolan-2-yl]pyrimidin-2-one · ligand · 3 copies · chains P, A
SO4 · Sulfate ion · ion · 7 copies · chains P, A

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	270	0.68	0.84	38	empty
2	617	0.65	0.75	44	SO4
3	224	0.59	0.80	27	empty
4	110	0.45	0.78	24	empty
5	164	0.41	0.73	25	FA2

Interfaces

1 interface between chains.

P–A · 839 Å² buried · 24 hydrogen bonds · protein-nucleic

Compared structures

6MU5 · Bst DNA polymerase I TNA/DNA binary complex · the same entry in another collection · chain P against P, 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 E1C9K5
Elsewhere: RCSB PDB 6MU5 · PDBe 6MU5 · UniProt E1C9K5

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