MolNFT v1 · #159724 · protein

Crystal structure of mtb aspartate decarboxylase in active form

6OZ8 · Aspartate 1 decarboxylase beta chain: “Crystal structure of mtb aspartate decarboxylase in active form”. X-ray diffraction, 1 ligand (PYR), 7 pockets (best druggability 0.72). MolNFT v1 #159724 on GenesisL1: 3D structure, binding…

PDB: 6OZ8
Type: protein
Length: 686 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspartate 1 decarboxylase beta chain; Aspartate 1 decarboxylase alpha chain
EC: 4.1.1.11
UniProt: P9WIL3
Ligands: PYR
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, I, E, K, G	Aspartate 1 decarboxylase beta chain	protein	24	0% helix, 67% strand	P9WIL3
B, J, F, H	Aspartate 1 decarboxylase alpha chain (EC 4.1.1.11)	protein	90	18% helix, 43% strand	P9WIL3
D, L	Aspartate 1 decarboxylase alpha chain (EC 4.1.1.11)	protein	91	18% helix, 42% strand	P9WIL3

Ligands and binding sites

PYR · Pyruvic acid · ligand · 6 copies · chains B, D, J, F, L, H

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.72	0.97	19	PYR
2	55	0.67	0.96	18	PYR
3	147	0.41	0.74	27	empty
4	113	0.40	0.76	20	empty
5	119	0.39	0.75	17	empty

Interfaces

20 interfaces between chains.

E–F · 1661 Å² buried · 35 hydrogen bonds · protein-protein
I–J · 1660 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 1656 Å² buried · 37 hydrogen bonds · protein-protein
K–L · 1650 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 1648 Å² buried · 36 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent (covalent ligand).

Compared structures

6OZ8 · Crystal structure of Mtb aspartate decarboxylase in active form · the same entry in another collection · chain G against G, 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 P9WIL3
Elsewhere: RCSB PDB 6OZ8 · PDBe 6OZ8 · UniProt P9WIL3

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