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Structure of glda from E.COLI

Analyse Structure of glda from E.COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZXL
Type: protein
Length: 1,468 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycerol dehydrogenase
EC: 1.1.1.6
UniProt: P0A9S5
Ligands: ZN, SO4, CL
Pockets: 13 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glycerol dehydrogenase (EC 1.1.1.6)	protein	367	57% helix, 14% strand	P0A9S5

Ligands and binding sites

ZN · Zinc ion · metal · 5 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 5 copies · chains B, C, D
CL · Chloride ion · ion · chains D
GOL · Glycerol · additive · 12 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	391	0.70	0.82	55	empty
2	577	0.69	0.78	56	GOL
3	693	0.68	0.76	56	GOL
4	365	0.68	0.81	51	empty
5	602	0.68	0.77	60	ZN, GOL

Interfaces

5 interfaces between chains.

A–B · 1430 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 1375 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 571 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 555 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 24 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

5ZXL · Structure of GldA from E.coli · the same entry in another collection · chain D against D, TM-score 1.00
P0A9S5 · AlphaFold monomer V2.0 prediction for glycerol dehydrogenase (P0A9S5) · 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 P0A9S5
Elsewhere: RCSB PDB 5ZXL · PDBe 5ZXL · UniProt P0A9S5

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