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Crystal structure of 2, 3-dihydroxybenzoic acid decarboxylase from fusarium oxysporum in complex with catechol

Analyse Crystal structure of 2, 3-dihydroxybenzoic acid decarboxylase from fusarium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BP1
Type: protein
Length: 1,338 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2,3-dihydroxybenzoate decarboxylase
UniProt: A0A420U2F4
Ligands: CAQ, ZN
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	2,3-dihydroxybenzoate decarboxylase	protein	336	53% helix, 13% strand	A0A420U2F4
C	2,3-dihydroxybenzoate decarboxylase	protein	335	53% helix, 13% strand	A0A420U2F4
D	2,3-dihydroxybenzoate decarboxylase	protein	331	54% helix, 13% strand	A0A420U2F4

Ligands and binding sites

CAQ · Catechol · ligand · 3 copies · chains A, D, B, C
ZN · Zinc ion · metal · chains C

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	226	0.84	0.97	46	empty
2	220	0.83	0.96	47	empty
3	925	0.74	0.78	111	empty
4	363	0.71	0.83	48	empty
5	124	0.52	0.81	21	empty

Interfaces

6 interfaces between chains.

B–C · 3003 Å² buried · 38 hydrogen bonds · protein-protein
A–D · 2998 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 812 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 775 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 115 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7BP1 · Crystal structure of 2, 3-dihydroxybenzoic acid decarboxylase from Fusarium oxysporum in… · 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 A0A420U2F4
Elsewhere: RCSB PDB 7BP1 · PDBe 7BP1 · UniProt A0A420U2F4

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