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

Analyse 323 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: 6KQK
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 0.81

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	805	0.81	0.84	95	NAI, 9TY
2	902	0.79	0.82	101	MG, NAI, 9TY
3	935	0.79	0.81	99	NAI, 9TY
4	1198	0.79	0.80	131	MG, NAI, 9TY
5	667	0.79	0.83	70	MG, NAI, 9TY

Interfaces

30 interfaces between chains.

K–L · 5752 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 5743 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 5739 Å² buried · 30 hydrogen bonds · protein-protein
G–H · 5722 Å² buried · 29 hydrogen bonds · protein-protein
E–F · 5704 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

6KQK · 323 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 6KQK · PDBe 6KQK · UniProt A0A157T175

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