MolNFT v1 · #32903 · protein

Native precursor of pyruvoyl dependent aspartate decarboxylase

2C45 · Aspartate 1-decarboxylase: “Native precursor of pyruvoyl dependent aspartate decarboxylase”. X-ray diffraction, 6 pockets (best druggability 0.80). MolNFT v1 #32903 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2C45
Type: protein
Length: 904 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: P9WIL3
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Aspartate 1-decarboxylase (EC 4.1.1.11)	protein	113	10% helix, 42% strand	P9WIL3

Pockets

6 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	953	0.80	0.82	68	empty
2	922	0.80	0.82	68	empty
3	71	0.37	0.77	19	empty
4	67	0.35	0.77	18	empty
5	52	0.31	0.76	14	empty

Interfaces

8 interfaces between chains.

F–G · 1038 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1038 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 1024 Å² buried · 14 hydrogen bonds · protein-protein
E–H · 1017 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 1002 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

2C45 · Native precursor of pyruvoyl dependent aspartate decarboxylase · the same entry in another collection · chain H against H, TM-score 1.00
P9WIL3 · AlphaFold monomer V2.0 prediction for aspartate 1-decarboxylase (P9WIL3) · a predicted model of the same protein · chain A 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 P9WIL3
Elsewhere: RCSB PDB 2C45 · PDBe 2C45 · UniProt P9WIL3

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