MolNFT v1 · #146025 · protein

Crystal structure of L,D-transpeptidase 5 from mycobacterium tuberculosis in apo form

6D5A: “Crystal structure of L,D-transpeptidase 5 from mycobacterium tuberculosis in apo form”. X-ray diffraction, 2 pockets (best druggability 0.49). MolNFT v1 #146025 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6D5A
Type: protein
Length: 347 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L,D-transpeptidase 5
EC: 2.3.2.-
UniProt: P9WKV3
Pockets: 2 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L,D-transpeptidase 5 (EC 2.3.2.-)	protein	347	9% helix, 42% strand	P9WKV3

Ligands and binding sites

PG4 · Tetraethylene glycol · additive · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	128	0.49	0.79	21	empty
2	60	0.30	0.75	15	empty

Compared structures

6D5A · Crystal structure of L,D-transpeptidase 5 from Mycobacterium tuberculosis in apo form · the same entry in another collection · chain A against A, TM-score 1.00
P9WKV3 · AlphaFold monomer V2.0 prediction for L,D-transpeptidase 5 (P9WKV3) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P9WKV3
Elsewhere: RCSB PDB 6D5A · PDBe 6D5A · UniProt P9WKV3

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