MolNFT v1 · #152976 · protein

Crystal structure of deaminase amne from pseudomonas sp. ap-3

6IZH · 2-aminomuconate deaminase: “Crystal structure of deaminase amne from pseudomonas sp. ap-3”. X-ray diffraction, 1 ligand (MG), 13 pockets (best druggability 0.79). MolNFT v1 #152976 on GenesisL1: 3D structure, binding sites and…

PDB: 6IZH
Type: protein
Length: 1,212 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-aminomuconate deaminase
EC: 3.5.99.5
UniProt: Q9KWS2
Ligands: MG
Pockets: 13 · best druggability 0.79

Structure

x-ray diffraction · 5 distinct chains · 25% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	2-aminomuconate deaminase (EC 3.5.99.5)	protein	138	23% helix, 29% strand	Q9KWS2
B, G, H	2-aminomuconate deaminase (EC 3.5.99.5)	protein	135	23% helix, 30% strand	Q9KWS2
D, F	2-aminomuconate deaminase (EC 3.5.99.5)	protein	137	26% helix, 29% strand	Q9KWS2
E	2-aminomuconate deaminase (EC 3.5.99.5)	protein	121	29% helix, 35% strand	Q9KWS2
I	2-aminomuconate deaminase (EC 3.5.99.5)	protein	136	26% helix, 29% strand	Q9KWS2

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains C, E

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

Pockets

13 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	863	0.79	0.82	90	empty
2	508	0.78	0.85	57	empty
3	110	0.77	0.97	27	empty
4	93	0.76	0.97	27	empty
5	723	0.76	0.81	81	empty

Interfaces

20 interfaces between chains.

G–H · 1048 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1044 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1044 Å² buried · 11 hydrogen bonds · protein-protein
G–I · 1043 Å² buried · 13 hydrogen bonds · protein-protein
D–F · 1037 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6IZH · Crystal structure of deaminase AmnE from Pseudomonas sp. AP-3 · the same entry in another collection · chain I against I, TM-score 1.00
Q9KWS2 · AlphaFold monomer V2.0 prediction for 2-aminomuconate deaminase (Q9KWS2) · a predicted model of the same protein · chain H 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 Q9KWS2
Elsewhere: RCSB PDB 6IZH · PDBe 6IZH · UniProt Q9KWS2

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