Research workbench

Vanyb in complex with D-alanine-D-alanine

Analyse Vanyb in complex with D-alanine-D-alanine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZHW
Type: protein
Length: 362 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-alanyl-D-alanine carboxypeptidase
EC: 3.4.16.4
UniProt: Q47746
Ligands: DAL, CU
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4)	protein	181	49% helix, 14% strand	Q47746

Ligands and binding sites

DAL · D-alanine · ligand · 4 copies · chains A, B
CU · Copper (II) ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B
PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B

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

Pockets

5 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	778	0.75	0.80	88	CU, DAL, PG4
2	85	0.49	0.83	18	empty
3	101	0.48	0.80	20	empty
4	103	0.45	0.79	18	GOL
5	72	0.41	0.80	15	GOL

Interfaces

1 interface between chains.

A–B · 1002 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (engineered).

Compared structures

5ZHW · VanYB in complex with D-Alanine-D-Alanine · the same entry in another collection · chain A against A, TM-score 1.00
Q47746 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase (Q47746) · 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 Q47746
Elsewhere: RCSB PDB 5ZHW · PDBe 5ZHW · UniProt Q47746

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