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Mutant endolysin from bacillus subtilis

Analyse Mutant endolysin from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HMB
Type: protein
Length: 464 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-acetylmuramoyl-L-alanine amidase xlya
EC: 3.5.1.28
UniProt: P39800
Ligands: ZN
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	N-acetylmuramoyl-L-alanine amidase xlya (EC 3.5.1.28)	protein	154	31% helix, 17% strand	P39800
B	N-acetylmuramoyl-L-alanine amidase xlya (EC 3.5.1.28)	protein	156	31% helix, 17% strand	P39800

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A, B, C

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

Pockets

4 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	566	0.66	0.77	58	empty
2	72	0.30	0.74	19	empty
3	72	0.29	0.73	18	empty
4	52	0.27	0.74	13	empty

Interfaces

2 interfaces between chains.

A–B · 537 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 390 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3HMB · Mutant endolysin from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
P39800 · AlphaFold monomer V2.0 prediction for N-acetylmuramoyl-L-alanine amidase xlya (P39800) · 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 P39800
Elsewhere: RCSB PDB 3HMB · PDBe 3HMB · UniProt P39800

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