MolNFT v1 · #172914 · protein + DNA

Muts in intermediate state

7AI7 · DNA mismatch repair protein muts: “Muts in intermediate state”. Electron microscopy, 1 ligand (ADP), 16 pockets (best druggability 0.77). MolNFT v1 #172914 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7AI7
Type: protein + DNA
Length: 1,487 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA mismatch repair protein muts; DNA (5'-D(P*GP*AP*TP*CP*CP*TP*AP*AP*CP*TP*AP*AP*G)-3')…
UniProt: P23909
Ligands: ADP
Pockets: 16 · best druggability 0.77

Structure

electron microscopy · 4 distinct chains · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA mismatch repair protein muts	protein	791	45% helix, 17% strand	P23909
B	DNA mismatch repair protein muts	protein	669	48% helix, 16% strand	P23909
C	DNA (5'-D(PGPAPTPCPCPTPAPAPCPTPAPAP*G)-3')	dna	13	—	—
D	DNA (5'-D(PCPTPTPAPGPCPTPTPAPGPGPAPTPC)-3')	dna	14	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B

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

Pockets

16 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	1183	0.77	0.79	94	empty
2	1018	0.74	0.77	69	empty
3	359	0.71	0.83	39	ADP
4	180	0.68	0.87	28	ADP
5	351	0.61	0.77	34	empty

Interfaces

6 interfaces between chains.

A–B · 3969 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 699 Å² buried · 63 hydrogen bonds · nucleic-nucleic
A–C · 595 Å² buried · 6 hydrogen bonds · protein-nucleic
A–D · 459 Å² buried · 7 hydrogen bonds · protein-nucleic
B–D · 185 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

7AI7 · MutS in Intermediate state · 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 B against A, TM-score 0.79

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 7AI7 · PDBe 7AI7 · UniProt P23909

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