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328 K cryoem structure of sso-kari in complex with MG2+, NADH and cpd

Analyse 328 K cryoem structure of sso-kari in complex with MG2+, NADH and cpd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KQO
Type: protein
Length: 3,936 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ketol-acid reductoisomerase
UniProt: A0A157T175
Ligands: NAI, 9TY, MG
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 1 distinct chain · 56% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	Ketol-acid reductoisomerase	protein	328	56% helix, 12% strand	A0A157T175

Ligands and binding sites

NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
9TY · cyclopropane-1,1-dicarboxylic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
MG · Magnesium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	654	0.79	0.84	75	MG, NAI, 9TY
2	673	0.79	0.83	75	MG, NAI, 9TY
3	683	0.78	0.83	75	MG, NAI, 9TY
4	650	0.78	0.83	76	MG, NAI, 9TY
5	656	0.77	0.82	68	MG, NAI, 9TY

Interfaces

30 interfaces between chains.

A–B · 5690 Å² buried · 26 hydrogen bonds · protein-protein
K–L · 5682 Å² buried · 26 hydrogen bonds · protein-protein
I–J · 5674 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 5672 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 5662 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

6KQO · 328 K cryoEM structure of Sso-KARI in complex with Mg2+, NADH and CPD · the same entry in another collection · chain A against A, 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 A0A157T175
Elsewhere: RCSB PDB 6KQO · PDBe 6KQO · UniProt A0A157T175

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