MolNFT v1 · #138174 · protein

Corynebacterium glutamicum hydrolyzed homoserine kinase

5WAS: “Corynebacterium glutamicum hydrolyzed homoserine kinase”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.66). MolNFT v1 #138174 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5WAS
Type: protein
Length: 279 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Homoserine kinase
EC: 2.7.1.39
UniProt: P07128
Ligands: PO4
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Homoserine kinase (EC 2.7.1.39)	protein	180	26% helix, 36% strand	P07128
B	Homoserine kinase (EC 2.7.1.39)	protein	37	43% helix, 24% strand	P07128
C	Homoserine kinase (EC 2.7.1.39)	protein	62	24% helix, 32% strand	P07128

Ligands and binding sites

PO4 · Phosphate ion · ion · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.66	0.95	23	empty
2	155	0.51	0.79	21	empty
3	122	0.45	0.78	34	PO4
4	55	0.28	0.74	12	empty

Interfaces

3 interfaces between chains.

A–C · 1813 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 542 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 314 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5WAS · Corynebacterium glutamicum Hydrolyzed Homoserine kinase · the same entry in another collection · chain B against B, TM-score 1.00
P07128 · AlphaFold monomer V2.0 prediction for homoserine kinase (P07128) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P07128
Elsewhere: RCSB PDB 5WAS · PDBe 5WAS · UniProt P07128

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