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Crystal structure of 2, 3-dihydroxybenzoic acid decarboxylase from Fusarium oxysporum

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: 6M53
Type: protein
Length: 1,333 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.55
Source: Fusarium oxysporum
Molecule: 2,3-dihydroxybenzoate decarboxylase
UniProt: A0A420U2F4
Ligands: ZN
Pockets: 15 · best druggability 0.82

Structure

x-ray diffraction · resolution 1.55 · 4 distinct chains · 54% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2,3-dihydroxybenzoate decarboxylase	protein	334	52% helix, 13% strand	A0A420U2F4
B	2,3-dihydroxybenzoate decarboxylase	protein	339	55% helix, 13% strand	A0A420U2F4
C	2,3-dihydroxybenzoate decarboxylase	protein	328	56% helix, 13% strand	A0A420U2F4
D	2,3-dihydroxybenzoate decarboxylase	protein	332	53% helix, 13% strand	A0A420U2F4

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 3 copies · chains B, D, C

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

Pockets

15 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	202	0.82	0.96	39	GOL
2	1042	0.75	0.78	109	empty
3	295	0.72	0.85	44	empty
4	370	0.67	0.81	56	empty
5	291	0.59	0.78	26	empty

Interfaces

4 interfaces between chains.

B–D · 3013 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 316 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 285 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 185 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6M53 · Crystal structure of 2, 3-dihydroxybenzoic acid decarboxylase from fusarium oxysporum · 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 6M53 · PDBe 6M53 · UniProt A0A420U2F4

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