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Structure of a 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase from burkholderia pseudomallei

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PDB: 3TK8
Type: protein
Length: 776 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase
EC: 2.3.1.117
UniProt: Q3JR17
Ligands: UNL, SO4
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase (EC 2.3.1.117)	protein	261	20% helix, 32% strand	Q3JR17
B	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase (EC 2.3.1.117)	protein	257	19% helix, 32% strand	Q3JR17
C	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase (EC 2.3.1.117)	protein	258	19% helix, 30% strand	Q3JR17

Ligands and binding sites

UNL · Unknown ligand · metal · 4 copies · chains A, B, C
SO4 · Sulfate ion · ion · 14 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, B

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

Pockets

7 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	622	0.73	0.80	72	SO4, UNL, EDO
2	556	0.68	0.77	59	EDO, SO4
3	592	0.67	0.77	61	SO4
4	93	0.42	0.79	24	empty
5	95	0.41	0.77	13	empty

Interfaces

3 interfaces between chains.

A–C · 1647 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1635 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1598 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

3TK8 · Structure of a 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q3JR17
Elsewhere: RCSB PDB 3TK8 · PDBe 3TK8 · UniProt Q3JR17

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