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Crystal structure of glycopeptide hexose oxidase DBV29 complexed with teicoplanin

Analyse Crystal structure of glycopeptide hexose oxidase DBV29 complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AWV
Type: protein
Length: 2,048 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative hexose oxidase; Teicoplanin
UniProt: Q7WZ62
Ligands: T55, N1L, FAD, MAN, NAG
Pockets: 17 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Putative hexose oxidase	protein	498	30% helix, 22% strand	Q7WZ62
I, J, K, L, M, N, O, P	Teicoplanin	protein	7	0% helix, 0% strand	—

Ligands and binding sites

T55 · 8-methylnonanoic acid · ligand · 6 copies · chains B, L, A, K, C, M, N, O, P
N1L · 2-amino-2-deoxy-beta-D-glucopyranuronic acid · ligand · 6 copies · chains A, K, B, L, C, M, N, O, P
FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, K, B, L, C, M, D
MAN · alpha-D-mannopyranose · sugar · 8 copies · chains B, I, C, J, K, L, M, N, A, O, P
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, I, C, J, A, K, L, M, N, O, P
CIT · Citric acid · additive · 5 copies · chains A, B, C, D, O

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

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	735	0.87	0.90	95	FAD, T55, N1L
2	731	0.87	0.90	94	FAD, T55, NAG, N1L
3	673	0.87	0.91	83	FAD, T55, N1L
4	948	0.85	0.87	87	empty
5	1125	0.85	0.85	105	FAD

Interfaces

14 interfaces between chains.

A–B · 1402 Å² buried · 13 hydrogen bonds · protein-protein
C–M · 623 Å² buried · 9 hydrogen bonds · protein-protein
A–K · 600 Å² buried · 9 hydrogen bonds · protein-protein
B–L · 584 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 445 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 56 modified, 16 glycan, 8 cofactor, 6 covalent, 1 disulfide (nonstandard, glycosylation, flavinylation, covalent ligand, disulfide).

Compared structures

5AWV · Crystal structure of glycopeptide hexose oxidase DBV29 complexed with teicoplanin · the same entry in another collection · chain B against B, 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 Q7WZ62
Elsewhere: RCSB PDB 5AWV · PDBe 5AWV · UniProt Q7WZ62

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