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Crystal structure of D-alanine-D-alanine ligase from helicobacter pylori

Analyse Crystal structure of D-alanine-D-alanine ligase from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PVP
Type: protein
Length: 644 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-alanine-D-alanine ligase
EC: 6.3.2.4
UniProt: Q2N4T5
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-alanine-D-alanine ligase (EC 6.3.2.4)	protein	329	32% helix, 28% strand	Q2N4T5
B	D-alanine-D-alanine ligase (EC 6.3.2.4)	protein	315	35% helix, 28% strand	Q2N4T5

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	806	0.71	0.76	72	empty
2	334	0.66	0.80	43	empty
3	362	0.65	0.80	54	empty
4	588	0.64	0.75	60	empty
5	65	0.32	0.75	14	empty

Interfaces

1 interface between chains.

A–B · 1570 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

2PVP · Crystal structure of D-Alanine-D-Alanine Ligase from Helicobacter pylori · 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 Q2N4T5
Elsewhere: RCSB PDB 2PVP · PDBe 2PVP · UniProt Q2N4T5

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