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Crystal structure of 4-ot from pseudomonas putida mt-2 with an enamine adduct on the N-terminal proline at 1.7 ångström resolution

Analyse Crystal structure of 4-ot from pseudomonas putida mt-2 with an enamine adduct… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4X1C
Type: protein
Length: 871 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-hydroxymuconate tautomerase
EC: 5.3.2.6
UniProt: Q01468
Ligands: NCO
Pockets: 12 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 44% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, N, O	2-hydroxymuconate tautomerase (EC 5.3.2.6)	protein	58	43% helix, 33% strand	Q01468
B	2-hydroxymuconate tautomerase (EC 5.3.2.6)	protein	56	45% helix, 32% strand	Q01468
C	2-hydroxymuconate tautomerase (EC 5.3.2.6)	protein	58	43% helix, 33% strand	Q01468
D, E	2-hydroxymuconate tautomerase (EC 5.3.2.6)	protein	59	42% helix, 32% strand	Q01468
F, I, J, M	2-hydroxymuconate tautomerase (EC 5.3.2.6)	protein	57	44% helix, 33% strand	Q01468
G	2-hydroxymuconate tautomerase (EC 5.3.2.6)	protein	61	48% helix, 31% strand	Q01468
H	2-hydroxymuconate tautomerase (EC 5.3.2.6)	protein	62	47% helix, 31% strand	Q01468
K, L	2-hydroxymuconate tautomerase (EC 5.3.2.6)	protein	57	42% helix, 33% strand	Q01468

Ligands and binding sites

NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains B, C, E, F

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

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1008	0.82	0.84	102	empty
2	1159	0.79	0.81	104	empty
3	165	0.50	0.77	22	empty
4	186	0.49	0.76	25	empty
5	142	0.44	0.76	21	empty

Interfaces

39 interfaces between chains.

G–J · 933 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 925 Å² buried · 7 hydrogen bonds · protein-protein
I–L · 908 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 899 Å² buried · 8 hydrogen bonds · protein-protein
H–K · 889 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (nonstandard).

Compared structures

4X1C · Crystal structure of 4-OT from Pseudomonas putida mt-2 with an enamine adduct on the… · the same entry in another collection · chain J against J, 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 Q01468
Elsewhere: RCSB PDB 4X1C · PDBe 4X1C · UniProt Q01468

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