MolNFT v1 · #61208 · protein

Structure of E. COLI dhdps mutant Y107W

3DEN · Dihydrodipicolinate synthase: “Structure of E. COLI dhdps mutant Y107W”. X-ray diffraction, 2 ligands (K, PO4), 3 pockets (best druggability 0.73). MolNFT v1 #61208 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3DEN
Type: protein
Length: 584 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydrodipicolinate synthase
EC: 4.2.1.52
UniProt: P0A6L2
Ligands: K, PO4
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dihydrodipicolinate synthase (EC 4.2.1.52)	protein	292	47% helix, 12% strand	P0A6L2

Ligands and binding sites

K · Potassium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 3 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	401	0.73	0.84	64	GOL
2	98	0.39	0.76	17	empty
3	105	0.38	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 1324 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

3DEN · Structure of E. coli DHDPS mutant Y107W · the same entry in another collection · chain A against A, TM-score 1.00
P0A6L2 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (P0A6L2) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P0A6L2
Elsewhere: RCSB PDB 3DEN · PDBe 3DEN · UniProt P0A6L2

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