MolNFT v1 · #95398 · protein

Putative aromatic acid decarboxylase

4IP2: “Putative aromatic acid decarboxylase”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.80). MolNFT v1 #95398 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4IP2
Type: protein
Length: 1,496 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aromatic acid decarboxylase
UniProt: Q9I6N5
Ligands: MG
Pockets: 10 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aromatic acid decarboxylase	protein	499	35% helix, 24% strand	Q9I6N5
B	Aromatic acid decarboxylase	protein	495	33% helix, 24% strand	Q9I6N5
C	Aromatic acid decarboxylase	protein	502	34% helix, 23% strand	Q9I6N5

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
GOL · Glycerol · additive · chains B

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	112	0.80	0.98	24	empty
2	909	0.79	0.82	62	EDO
3	988	0.79	0.81	65	EDO
4	1028	0.78	0.80	71	EDO
5	1001	0.77	0.79	95	empty

Interfaces

3 interfaces between chains.

A–B · 3611 Å² buried · 42 hydrogen bonds · protein-protein
A–C · 248 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 118 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4IP2 · Putative Aromatic Acid Decarboxylase · the same entry in another collection · chain A against A, TM-score 1.00
Q9I6N5 · AlphaFold monomer V2.0 prediction for ubid-like decarboxylase (Q9I6N5) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q9I6N5
Elsewhere: RCSB PDB 4IP2 · PDBe 4IP2 · UniProt Q9I6N5

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