MolNFT v1 · #16053 · protein + DNA

Crystal structure of the muts-ADPBEF3-DNA complex

1NNE · 5'- D(*GP*CP*GP*AP*CP*GP*CP*TP*AP*GP*CP*GP*TP*GP*CP*GP*GP*CP…: “Crystal structure of the muts-ADPBEF3-DNA complex”. X-ray diffraction, 3 ligands (BEF, ADP, SO4), 20 pockets (best druggability 0.78). MolNFT v1 #16053 on GenesisL1: 3D…

PDB: 1NNE
Type: protein + DNA
Length: 1,563 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'- D(*GP*CP*GP*AP*CP*GP*CP*TP*AP*GP*CP*GP*TP*GP*CP*GP*GP*CP*TP *CP*GP*TP*C)-3'; 5'…
UniProt: Q56215
Ligands: BEF, ADP, SO4
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'- D(GPCPGPAPCPGPCPTPAPGPCPGPTPGPCPGPGPCPTP CPGPTP*C)-3'	dna	23	—	—
D	5'- D(PGPGPAPCPGPAPGPCPCPGPCPCPGPCPTPAPGPCPG PTPCPG)-3'	dna	22	—	—
A	DNA mismatch repair protein muts	protein	759	45% helix, 19% strand	Q56215
B	DNA mismatch repair protein muts	protein	759	45% helix, 18% strand	Q56215

Ligands and binding sites

BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, B
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	923	0.78	0.81	94	BEF, ADP, EDO
2	938	0.72	0.77	66	empty
3	455	0.70	0.81	52	empty
4	344	0.63	0.79	28	empty
5	426	0.62	0.76	38	empty

Interfaces

6 interfaces between chains.

A–B · 2293 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1067 Å² buried · 81 hydrogen bonds · nucleic-nucleic
C–A · 605 Å² buried · 10 hydrogen bonds · protein-nucleic
D–B · 500 Å² buried · 9 hydrogen bonds · protein-nucleic
D–A · 468 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

1NNE · Crystal Structure of the MutS-ADPBeF3-DNA complex · the same entry in another collection · chain C against C, TM-score 1.00
Q56215 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein muts (Q56215) · a predicted model of the same protein · 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 Q56215
Elsewhere: RCSB PDB 1NNE · PDBe 1NNE · UniProt Q56215

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