MolNFT v1 · #119933 · protein

Crystal structure of the ketosynthase stld complexed with substrate

5GK1: “Crystal structure of the ketosynthase stld complexed with substrate”. X-ray diffraction, 1 ligand (2K3), 18 pockets (best druggability 0.79). MolNFT v1 #119933 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GK1
Type: protein
Length: 1,516 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ketosynthase stld
UniProt: Q7N4Z6
Ligands: 2K3
Pockets: 18 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ketosynthase stld	protein	379	38% helix, 24% strand	Q7N4Z6

Ligands and binding sites

2K3 · 3-oxo-5-methylhexanoic acid · ligand · 2 copies · chains A, C

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

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	116	0.79	0.97	32	2K3
2	117	0.78	0.96	33	2K3
3	422	0.77	0.86	97	empty
4	394	0.76	0.86	92	empty
5	173	0.75	0.91	40	empty

Interfaces

3 interfaces between chains.

C–D · 3016 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2984 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 612 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

5GK1 · Crystal structure of the ketosynthase StlD complexed with substrate · 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 Q7N4Z6
Elsewhere: RCSB PDB 5GK1 · PDBe 5GK1 · UniProt Q7N4Z6

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