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Crystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase N169D in complex with NAD+

Analyse Crystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase N169D in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KJ5
Type: protein
Length: 1,933 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-aminomuconate 6-semialdehyde dehydrogenase
UniProt: Q83V33
Ligands: NAD
Pockets: 12 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, C	2-aminomuconate 6-semialdehyde dehydrogenase	protein	483	42% helix, 24% strand	Q83V33
B	2-aminomuconate 6-semialdehyde dehydrogenase	protein	484	42% helix, 23% strand	Q83V33

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C

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

Pockets

12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	876	0.86	0.88	63	empty
2	1120	0.85	0.86	117	empty
3	344	0.85	0.94	44	empty
4	848	0.79	0.82	94	empty
5	631	0.76	0.82	60	empty

Interfaces

6 interfaces between chains.

B–C · 2606 Å² buried · 33 hydrogen bonds · protein-protein
A–D · 2582 Å² buried · 35 hydrogen bonds · protein-protein
D–C · 853 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 819 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 805 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5KJ5 · Crystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase N169D in complex with… · the same entry in another collection · chain A against A, 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 Q83V33
Elsewhere: RCSB PDB 5KJ5 · PDBe 5KJ5 · UniProt Q83V33

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