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Crystal structure of LDTMT2 from mycobacterium tuberculosis

Analyse Crystal structure of LDTMT2 from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RLG
Type: protein
Length: 702 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L,D-transpeptidase 2
EC: 2.3.2.-
UniProt: O53223
Ligands: NA, NO3
Pockets: 7 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	L,D-transpeptidase 2 (EC 2.3.2.-)	protein	351	9% helix, 44% strand	O53223

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A
NO3 · Nitrate ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B

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	579	0.68	0.78	41	NA
2	205	0.48	0.75	29	EDO
3	76	0.45	0.82	21	empty
4	83	0.43	0.80	21	empty
5	103	0.41	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 388 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6RLG · Crystal structure of LdtMt2 from Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
O53223 · AlphaFold monomer V2.0 prediction for L,D-transpeptidase 2 (O53223) · a predicted model of the same protein · 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 O53223
Elsewhere: RCSB PDB 6RLG · PDBe 6RLG · UniProt O53223

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