MolNFT v1 · #82695 · protein

Escherichia COLI pgab N-terminal domain

3VUS · Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase: “Escherichia COLI pgab N-terminal domain”. X-ray diffraction, 2 ligands (ZN, HG), 5 pockets (best druggability 0.59). MolNFT v1 #82695 on GenesisL1: 3D structure, binding sites and…

PDB: 3VUS
Type: protein
Length: 519 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
EC: 3.5.1.-
UniProt: P75906
Ligands: ZN, HG
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase (EC 3.5.1.-)	protein	263	37% helix, 21% strand	P75906
B	Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase (EC 3.5.1.-)	protein	256	38% helix, 22% strand	P75906

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
HG · Mercury (II) ion · metal · chains 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	404	0.59	0.76	39	empty
2	84	0.38	0.77	23	ZN, ACT
3	65	0.34	0.77	18	empty
4	62	0.33	0.77	22	ACT
5	56	0.29	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 668 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3VUS · Escherichia coli PgaB N-terminal domain · the same entry in another collection · chain A against A, TM-score 1.00
P75906 · AlphaFold monomer V2.0 prediction for poly-beta-1,6-N-acetyl-D- glucosamine N-deacetylase… · a predicted model of the same protein · chain A 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 P75906
Elsewhere: RCSB PDB 3VUS · PDBe 3VUS · UniProt P75906

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