MolNFT v1 · #128874 · protein

Crystal structure of apo klebsiella pneumoniae 3,4-dihydroxybenzoic acid decarboxylase (aroy)

5O3M · Protocatechuate decarboxylase: “Crystal structure of apo klebsiella pneumoniae 3,4-dihydroxybenzoic acid decarboxylase (aroy)”. X-ray diffraction, 1 ligand (9JE), 20 pockets (best druggability 0.76). MolNFT v1 #128874 on GenesisL1…

PDB: 5O3M
Type: protein
Length: 2,942 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protocatechuate decarboxylase
UniProt: B9A9M6
Ligands: 9JE
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 28% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protocatechuate decarboxylase	protein	493	29% helix, 26% strand	B9A9M6
B	Protocatechuate decarboxylase	protein	490	29% helix, 27% strand	B9A9M6
C	Protocatechuate decarboxylase	protein	489	27% helix, 26% strand	B9A9M6
D, E	Protocatechuate decarboxylase	protein	491	29% helix, 26% strand	B9A9M6
F	Protocatechuate decarboxylase	protein	488	27% helix, 27% strand	B9A9M6

Ligands and binding sites

9JE · pentane-1,5-diol · ligand · 10 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1095	0.76	0.78	72	empty
2	881	0.75	0.79	62	empty
3	885	0.75	0.79	66	empty
4	867	0.74	0.78	63	9JE
5	818	0.74	0.79	64	empty

Interfaces

12 interfaces between chains.

D–E · 3960 Å² buried · 48 hydrogen bonds · protein-protein
A–B · 3959 Å² buried · 44 hydrogen bonds · protein-protein
C–F · 3919 Å² buried · 44 hydrogen bonds · protein-protein
A–C · 1087 Å² buried · 16 hydrogen bonds · protein-protein
B–E · 1084 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5O3M · Crystal structure of apo Klebsiella pneumoniae 3,4-dihydroxybenzoic acid decarboxylase… · 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 B9A9M6
Elsewhere: RCSB PDB 5O3M · PDBe 5O3M · UniProt B9A9M6

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