MolNFT v1 · #25840 · protein + DNA

ATP bound muts

1W7A · DNA mismatch repair protein muts: “ATP bound muts”. X-ray diffraction, 2 ligands (ATP, MG), 18 pockets (best druggability 0.78). MolNFT v1 #25840 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1W7A
Type: protein + DNA
Length: 1,588 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA mismatch repair protein muts; 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP…
UniProt: P23909
Ligands: ATP, MG
Pockets: 18 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA mismatch repair protein muts	protein	791	46% helix, 19% strand	P23909
B	DNA mismatch repair protein muts	protein	762	48% helix, 18% strand	P23909
E	5'-D(APGPCPTPGPCPCPAPGPGP CPAPCPCPAPGPTPGPTPCPAPGPCPGPTPCPCPTP* AP*T)-3'	dna	18	—	—
F	5'-D(APTPAPGPGPAPCPGPCPTP GPAPCPAPCPTPGPGPTPGPCPTPTPGPGPCPAPGP* CP*T)-3'	dna	17	—	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · chains A

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

Pockets

18 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	925	0.78	0.81	100	empty
2	1085	0.76	0.78	122	ATP, MG
3	291	0.70	0.85	29	empty
4	361	0.70	0.83	53	empty
5	494	0.68	0.79	54	empty

Interfaces

6 interfaces between chains.

A–B · 2748 Å² buried · 35 hydrogen bonds · protein-protein
E–F · 813 Å² buried · 67 hydrogen bonds · nucleic-nucleic
A–F · 657 Å² buried · 10 hydrogen bonds · protein-nucleic
A–E · 656 Å² buried · 16 hydrogen bonds · protein-nucleic
B–E · 328 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

1W7A · ATP bound MutS · the same entry in another collection · chain A against A, TM-score 1.00
P23909 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein muts (P23909) · 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 P23909
Elsewhere: RCSB PDB 1W7A · PDBe 1W7A · UniProt P23909

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