MolNFT v1 · #142503 · protein

Vanyb in complex with D-alanine

6A6A · D-alanyl-D-alanine carboxypeptidase: “Vanyb in complex with D-alanine”. X-ray diffraction, 2 ligands (DAL, ZN), 5 pockets (best druggability 0.76). MolNFT v1 #142503 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6A6A
Type: protein
Length: 364 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, ZN
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4)	protein	183	48% helix, 14% strand	Q47746
B	D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4)	protein	181	48% helix, 14% strand	Q47746

Ligands and binding sites

DAL · D-alanine · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B
PGE · Triethylene glycol · additive · 4 copies · chains A, B
ACT · Acetate ion · 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	804	0.76	0.80	87	DAL, ACT, PGE, ZN
2	93	0.45	0.80	20	empty
3	69	0.45	0.82	16	empty
4	83	0.41	0.78	16	GOL
5	78	0.38	0.78	15	GOL

Interfaces

1 interface between chains.

A–B · 985 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6A6A · VanYB in complex with 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 B against A, TM-score 0.99

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 6A6A · PDBe 6A6A · UniProt Q47746

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