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Crystal structure of native 4-ot from pseudomonas putida mt-2 at 1.94 ångström

Analyse Crystal structure of native 4-ot from pseudomonas putida mt-2 at 1.94 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4X19
Type: protein
Length: 1,713 residues
Chains: 30
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: 20 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E, F, G, H, I, J, K, M, N, O, P, Q, R, T, U, W, X, Y, Z, b, c, d	2-hydroxymuconate tautomerase (EC 5.3.2.6)	protein	57	44% helix, 33% strand	Q01468
B, S, a	2-hydroxymuconate tautomerase (EC 5.3.2.6)	protein	56	45% helix, 32% strand	Q01468
L	2-hydroxymuconate tautomerase (EC 5.3.2.6)	protein	62	40% helix, 31% strand	Q01468
V	2-hydroxymuconate tautomerase (EC 5.3.2.6)	protein	58	43% helix, 33% strand	Q01468

Ligands and binding sites

NCO · Cobalt hexammine(iii) · ligand · chains 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	123	0.77	0.96	30	empty
2	345	0.76	0.87	46	empty
3	398	0.71	0.83	72	empty
4	914	0.70	0.76	90	empty
5	616	0.67	0.77	67	empty

Interfaces

80 interfaces between chains.

S–T · 928 Å² buried · 10 hydrogen bonds · protein-protein
O–P · 905 Å² buried · 16 hydrogen bonds · protein-protein
K–L · 902 Å² buried · 15 hydrogen bonds · protein-protein
Y–Z · 901 Å² buried · 9 hydrogen bonds · protein-protein
Q–R · 897 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4X19 · Crystal structure of native 4-OT from Pseudomonas putida mt-2 at 1.94 Angstrom · the same entry in another collection · chain K against K, 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 4X19 · PDBe 4X19 · UniProt Q01468

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