Research workbench

Muts in complex with the N-terminal domain of mutl - crystal form 1

Analyse Muts in complex with the N-terminal domain of mutl - crystal form 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AKB
Type: protein
Length: 2,769 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA mismatch repair protein muts; DNA mismatch repair protein mutl
UniProt: P23909, P23367
Ligands: ANP
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA mismatch repair protein muts	protein	663	48% helix, 16% strand	P23909
C, D, F	DNA mismatch repair protein mutl	protein	285	37% helix, 26% strand	P23367
E	DNA mismatch repair protein muts	protein	588	45% helix, 14% strand	P23909

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains A, B, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1046	0.80	0.82	120	ANP
2	955	0.77	0.79	91	empty
3	75	0.75	0.98	23	empty
4	71	0.75	0.98	24	empty
5	778	0.75	0.80	64	empty

Interfaces

8 interfaces between chains.

A–B · 3171 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 689 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 668 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 640 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 460 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5AKB · MutS in complex with the N-terminal domain of MutL - crystal form 1 · the same entry in another collection · chain F against F, TM-score 1.00
P23367 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein mutl (P23367) · a predicted model of the same protein · chain C against A, TM-score 0.87
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 0.79

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
Every structure of UniProt P23367
Elsewhere: RCSB PDB 5AKB · PDBe 5AKB · UniProt P23909 · UniProt P23367

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