MolNFT v1 · #135432 · protein + DNA

DNA polymerase mu reactant complex, MN2+ (10 min)

5TYW · DNA-directed DNA/RNA polymerase mu: “DNA polymerase mu reactant complex, MN2+ (10 min)”. X-ray diffraction, 4 ligands (TTP, PPV, MN), 2 pockets (best druggability 0.73). MolNFT v1 #135432 on GenesisL1: 3D structure, binding sites…

PDB: 5TYW
Type: protein + DNA
Length: 345 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed DNA/RNA polymerase mu; DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3'); DNA…
EC: 2.7.7.7
UniProt: Q9NP87
Ligands: TTP, PPV, MN, NA
Pockets: 2 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed DNA/RNA polymerase mu (EC 2.7.7.7)	protein	327	52% helix, 14% strand	Q9NP87
T	DNA (5'-D(CPGPGPCPAPTPAPCP*G)-3')	dna	9	—	—
P	DNA (5'-D(CPGPTPAP*T)-3')	dna	5	—	—
D	DNA (5'-D(PGPCPCPG)-3')	dna	4	—	—

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · chains A, T, P
PPV · Pyrophosphate · ligand · chains A, P
MN · Manganese (II) ion · metal · 6 copies · chains A, P, T
NA · Sodium ion · metal · chains A, P
EDO · 1,2-ethanediol · additive · 4 copies · chains A, T, P
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1084	0.73	0.76	54	PPV, MN, DTT
2	56	0.36	0.80	12	empty

Interfaces

5 interfaces between chains.

A–T · 698 Å² buried · 19 hydrogen bonds · protein-nucleic
A–P · 578 Å² buried · 18 hydrogen bonds · protein-nucleic
A–D · 429 Å² buried · 16 hydrogen bonds · protein-nucleic
T–P · 255 Å² buried · 20 hydrogen bonds · nucleic-nucleic
T–D · 198 Å² buried · 19 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 covalent (additive adduct, covalent ligand).

Compared structures

5TYW · DNA Polymerase Mu Reactant Complex, Mn2+ (10 min) · the same entry in another collection · chain A against A, TM-score 1.00
Q9NP87 · AlphaFold monomer V2.0 prediction for DNA-directed DNA/RNA polymerase mu (Q9NP87) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9NP87
Elsewhere: RCSB PDB 5TYW · PDBe 5TYW · UniProt Q9NP87

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