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Crystal structure of escherichia COLI gadb (neutral pH)

Analyse Crystal structure of escherichia COLI gadb (neutral pH) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PMO
Type: protein
Length: 2,743 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate decarboxylase beta
EC: 4.1.1.15
UniProt: P69910
Ligands: PLR
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate decarboxylase beta (EC 4.1.1.15)	protein	455	38% helix, 18% strand	P69910
B, E	Glutamate decarboxylase beta (EC 4.1.1.15)	protein	463	39% helix, 16% strand	P69910
C, D, F	Glutamate decarboxylase beta (EC 4.1.1.15)	protein	454	39% helix, 18% strand	P69910

Ligands and binding sites

PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 6 copies · chains A, B, C, D, E, F
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 18 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1117	0.83	0.84	94	TRS
2	1189	0.83	0.84	99	empty
3	622	0.81	0.86	65	empty
4	62	0.73	0.99	26	PLR
5	61	0.73	0.99	21	PLR

Interfaces

12 interfaces between chains.

E–F · 5702 Å² buried · 79 hydrogen bonds · protein-protein
C–D · 5665 Å² buried · 76 hydrogen bonds · protein-protein
A–B · 5664 Å² buried · 80 hydrogen bonds · protein-protein
B–C · 2540 Å² buried · 36 hydrogen bonds · protein-protein
D–E · 2290 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

1PMO · Crystal structure of Escherichia coli GadB (neutral pH) · the same entry in another collection · chain F against F, TM-score 1.00
P69910 · AlphaFold monomer V2.0 prediction for glutamate decarboxylase beta (P69910) · a predicted model of the same protein · chain F against A, TM-score 0.97

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 P69910
Elsewhere: RCSB PDB 1PMO · PDBe 1PMO · UniProt P69910

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