MolNFT v1 · #116971 · protein

Crystal structure of LDTMT2 at 1.79 ångström resolution

5DU7 · L,D-transpeptidase 2: “Crystal structure of LDTMT2 at 1.79 ångström resolution”. X-ray diffraction, 16 pockets (best druggability 0.56). MolNFT v1 #116971 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DU7
Type: protein
Length: 1,399 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L,D-transpeptidase 2
EC: 2.3.2.-
UniProt: O53223
Pockets: 16 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L,D-transpeptidase 2 (EC 2.3.2.-)	protein	350	9% helix, 44% strand	O53223
B, D	L,D-transpeptidase 2 (EC 2.3.2.-)	protein	349	9% helix, 44% strand	O53223
C	L,D-transpeptidase 2 (EC 2.3.2.-)	protein	351	9% helix, 44% strand	O53223

Pockets

16 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	64	0.56	0.88	17	empty
2	163	0.49	0.77	28	empty
3	102	0.49	0.81	20	empty
4	100	0.48	0.81	17	empty
5	149	0.47	0.77	28	empty

Interfaces

3 interfaces between chains.

B–C · 879 Å² buried · 3 hydrogen bonds · protein-protein
D–C · 513 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 507 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5DU7 · Crystal structure of ldtMt2 at 1.79 Angstrom resolution · 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 5DU7 · PDBe 5DU7 · UniProt O53223

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