MolNFT v1 · #74361 · protein

Crystal structure of cleaved L-aspartate-alpha-decarboxylase from francisella tularensis

3OUG · Aspartate 1-decarboxylase: “Crystal structure of cleaved L-aspartate-alpha-decarboxylase from francisella tularensis”. X-ray diffraction, 1 ligand (CL), 14 pockets (best druggability 0.86). MolNFT v1 #74361 on GenesisL1: 3D…

PDB: 3OUG
Type: protein
Length: 854 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspartate 1-decarboxylase
EC: 4.1.1.11
UniProt: Q5NF56
Ligands: CL
Pockets: 14 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F, G, H, I	Aspartate 1-decarboxylase (EC 4.1.1.11)	protein	107	11% helix, 50% strand	Q5NF56
C, E	Aspartate 1-decarboxylase (EC 4.1.1.11)	protein	106	11% helix, 51% strand	Q5NF56

Ligands and binding sites

CL · Chloride ion · ion · 8 copies · chains A, C, B, E, F, I, G, H
GOL · Glycerol · additive · 6 copies · chains A, B, E, C, F, H, I, G

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

Pockets

14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	677	0.86	0.90	61	GOL
2	682	0.86	0.90	61	GOL
3	66	0.52	0.86	16	empty
4	53	0.47	0.86	16	empty
5	69	0.36	0.77	23	empty

Interfaces

19 interfaces between chains.

G–H · 1101 Å² buried · 21 hydrogen bonds · protein-protein
F–I · 1095 Å² buried · 19 hydrogen bonds · protein-protein
F–H · 1086 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1084 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 1083 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

3OUG · Crystal structure of cleaved L-aspartate-alpha-decarboxylase from Francisella tularensis · the same entry in another collection · chain I against I, TM-score 1.00
Q5NF56 · AlphaFold monomer V2.0 prediction for aspartate 1-decarboxylase (Q5NF56) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 Q5NF56
Elsewhere: RCSB PDB 3OUG · PDBe 3OUG · UniProt Q5NF56

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