MolNFT v1 · #141564 · protein

Structure of glycolate oxidase without FMN from nicotiana benthamiana

5ZBN: “Structure of glycolate oxidase without FMN from nicotiana benthamiana”. X-ray diffraction, 1 ligand (PO4), 14 pockets (best druggability 0.78). MolNFT v1 #141564 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZBN
Type: protein
Length: 1,039 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycolate oxidase
UniProt: E1AXT8
Ligands: PO4
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycolate oxidase	protein	359	40% helix, 13% strand	E1AXT8
B	Glycolate oxidase	protein	347	41% helix, 14% strand	E1AXT8
C	Glycolate oxidase	protein	333	41% helix, 14% strand	E1AXT8

Ligands and binding sites

PO4 · Phosphate ion · ion · 3 copies · chains A, B, C

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

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	471	0.78	0.86	52	PO4
2	511	0.74	0.82	51	PO4
3	505	0.73	0.82	54	PO4
4	212	0.55	0.79	32	empty
5	167	0.49	0.77	22	empty

Interfaces

3 interfaces between chains.

A–C · 401 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 320 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 170 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5ZBN · Structure of glycolate oxidase without FMN from Nicotiana benthamiana · the same entry in another collection · 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 E1AXT8
Elsewhere: RCSB PDB 5ZBN · PDBe 5ZBN · UniProt E1AXT8

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