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L,D-transpeptidase from mycobacterium smegmatis

Analyse L,D-transpeptidase from mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XVO
Type: protein
Length: 651 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L,D-transpeptidase
UniProt: I7G323
Ligands: PO4
Pockets: 8 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	L,D-transpeptidase	protein	217	11% helix, 44% strand	I7G323

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains A, B, C

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	163	0.66	0.86	32	PO4
2	168	0.64	0.85	34	PO4
3	140	0.52	0.80	28	PO4
4	177	0.45	0.75	30	empty
5	151	0.43	0.75	29	empty

Interfaces

2 interfaces between chains.

A–B · 639 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 637 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified (engineered).

Compared structures

4XVO · L,D-transpeptidase from Mycobacterium smegmatis · the same entry in another collection · 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 I7G323
Elsewhere: RCSB PDB 4XVO · PDBe 4XVO · UniProt I7G323

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