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2.5 ångströms X-ray crystal structure of of human 2-amino-3- carboxymuconate-6-semialdehyde decarboxylase in complex with dipicolinic acid

Analyse 2.5 ångströms X-ray crystal structure of of human 2-amino-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IH3
Type: protein
Length: 1,992 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
EC: 4.1.1.45
UniProt: Q8TDX5
Ligands: PDC, ZN
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (EC 4.1.1.45)	protein	332	42% helix, 17% strand	Q8TDX5

Ligands and binding sites

PDC · Pyridine-2,6-dicarboxylic acid · ligand · 6 copies · chains A, F, B, C, D, E
ZN · Zinc ion · metal · 6 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, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	753	0.76	0.80	51	empty
2	395	0.69	0.81	55	PDC
3	446	0.69	0.80	62	PDC
4	376	0.69	0.81	51	PDC
5	262	0.69	0.84	26	empty

Interfaces

6 interfaces between chains.

D–E · 2571 Å² buried · 28 hydrogen bonds · protein-protein
A–F · 2549 Å² buried · 38 hydrogen bonds · protein-protein
B–C · 2546 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 494 Å² buried · 3 hydrogen bonds · protein-protein
B–E · 187 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4IH3 · 2.5 Angstroms X-ray crystal structure of of human… · the same entry in another collection · chain F against F, TM-score 1.00
Q8TDX5 · AlphaFold monomer V2.0 prediction for 2-amino-3-carboxymuconate-6-semialdehyde… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q8TDX5
Elsewhere: RCSB PDB 4IH3 · PDBe 4IH3 · UniProt Q8TDX5

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