MolNFT v1 · #91754 · protein

Structure of the C-terminal domain of the saccharomyces cerevisiae mutl alpha (MLH1/PMS1) heterodimer bound to a fragment of EXO1

4FMO · DNA mismatch repair protein MLH1: “Structure of the C-terminal domain of the saccharomyces cerevisiae mutl alpha (MLH1/PMS1) heterodimer bound…”. X-ray diffraction, 2 ligands (ZN, MG), 7 pockets (best druggability 0.54). MolNFT v1…

PDB: 4FMO
Type: protein
Length: 479 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA mismatch repair protein MLH1; DNA mismatch repair protein PMS1; DNA repair peptide
UniProt: P38920, P14242, P39875
Ligands: ZN, MG
Pockets: 7 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA mismatch repair protein MLH1	protein	264	51% helix, 17% strand	P38920
B	DNA mismatch repair protein PMS1	protein	208	38% helix, 24% strand	P14242
C	DNA repair peptide	protein	7	0% helix, 0% strand	P39875

Ligands and binding sites

ZN · Zinc ion · metal · 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

7 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	217	0.54	0.78	26	empty
2	85	0.49	0.83	17	empty
3	52	0.33	0.78	16	empty
4	98	0.32	0.72	20	empty
5	79	0.32	0.74	16	empty

Interfaces

2 interfaces between chains.

A–B · 1883 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 433 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4FMO · Structure of the C-terminal domain of the Saccharomyces cerevisiae MUTL alpha (MLH1/PMS1)… · the same entry in another collection · chain A against A, TM-score 1.00
P38920 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein MLH1 (P38920) · a predicted model of the same protein · chain A against A, TM-score 0.96
P14242 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein PMS1 (P14242) · a predicted model of the same protein · chain B against A, TM-score 0.88
P39875 · AlphaFold monomer V2.0 prediction for exodeoxyribonuclease 1 (P39875) · a predicted model of the same protein · chain C against A, TM-score 0.61

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 P38920
Every structure of UniProt P14242
Every structure of UniProt P39875
Elsewhere: RCSB PDB 4FMO · PDBe 4FMO · UniProt P38920 · UniProt P14242 · UniProt P39875

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