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Crystal structure of the suca domain of mycobacterium smegmatis kgd cocrystallized with succinylphosphonate

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: 6R29
Type: protein
Length: 1,702 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: QSP, MG
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 44% 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	847	44% 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

QSP · (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-oxidanyl-4-phosphono-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 · 5 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, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	829	0.87	0.89	134	QSP, MG
2	1116	0.80	0.81	96	MPD
3	720	0.73	0.79	63	MPD
4	589	0.70	0.79	70	empty
5	541	0.69	0.79	66	empty

Interfaces

1 interface between chains.

A–B · 5267 Å² buried · 104 hydrogen bonds · protein-protein

Compared structures

6R29 · 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

Analyse

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Every structure of UniProt A0R2B1
Elsewhere: RCSB PDB 6R29 · PDBe 6R29 · UniProt A0R2B1

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