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Crystal structure of the suca domain of mycobacterium smegmatis kgd cocrystallized with succinylphosphonate phosphonoethyl ester (pesp)

Analyse Crystal structure of the suca domain of mycobacterium smegmatis kgd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6R2A
Type: protein
Length: 1,701 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Multifunctional 2-oxoglutarate metabolism enzyme
EC: 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61
UniProt: A0R2B1
Ligands: ZP1, MG
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Multifunctional 2-oxoglutarate metabolism enzyme (EC 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61)	protein	846	43% helix, 15% strand	A0R2B1
B	Multifunctional 2-oxoglutarate metabolism enzyme (EC 2.2.1.5, 4.1.1.71, 1.2.4.2, 2.3.1.61)	protein	855	44% helix, 15% strand	A0R2B1

Ligands and binding sites

ZP1 · (4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy) phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-[ethoxy(oxidanyl)phosphoryl]-4-oxidanyl-butanoic acid · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 4 copies · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, B

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	1114	0.87	0.88	167	ZP1, MG
2	968	0.81	0.82	87	empty
3	602	0.73	0.80	54	MPD
4	431	0.70	0.81	63	empty
5	302	0.60	0.78	34	empty

Interfaces

1 interface between chains.

A–B · 5249 Å² buried · 111 hydrogen bonds · protein-protein

Compared structures

6R2A · Crystal structure of the SucA domain of Mycobacterium smegmatis KGD cocrystallized with… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt A0R2B1
Elsewhere: RCSB PDB 6R2A · PDBe 6R2A · UniProt A0R2B1

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