Research workbench

PVC-AT

Analyse PVC-AT in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XF2
Type: protein
Length: 1,376 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase
EC: 1.11.1.6
Ligands: HDD, 3TR, NAG, CA
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Catalase (EC 1.11.1.6)	protein	688	33% helix, 16% strand	—

Ligands and binding sites

HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 2 copies · chains A, E
3TR · 3-amino-1,2,4-triazole · ligand · 2 copies · chains A, E
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, E
CA · Calcium ion · metal · 6 copies · chains A, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	501	0.84	0.91	105	CA
2	264	0.84	0.95	40	HDD, 3TR
3	261	0.84	0.95	37	HDD, 3TR
4	1083	0.83	0.84	113	empty
5	181	0.65	0.85	42	empty

Interfaces

1 interface between chains.

A–E · 6337 Å² buried · 105 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 glycan, 2 covalent (N-glycosylation, covalent ligand).

Compared structures

2XF2 · PVC-AT · 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
Elsewhere: RCSB PDB 2XF2 · PDBe 2XF2

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