MolNFT v1 · #140765 · protein

Crystal structure of dodecameric dehydroquinate dehydratase from acinetobacter baumannii at 1.9A resolution

5YL5 · 3-dehydroquinate dehydratase: “Crystal structure of dodecameric dehydroquinate dehydratase from acinetobacter baumannii at 1.9A resolution”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.73). MolNFT v1 #140765…

PDB: 5YL5
Type: protein
Length: 1,742 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-dehydroquinate dehydratase
EC: 4.2.1.10
UniProt: A3M692
Ligands: SO4
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, L	3-dehydroquinate dehydratase (EC 4.2.1.10)	protein	145	48% helix, 17% strand	A3M692
K	3-dehydroquinate dehydratase (EC 4.2.1.10)	protein	147	47% helix, 16% strand	A3M692

Ligands and binding sites

SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D, E, F, G, H, L, I, J, K
GOL · Glycerol · additive · 4 copies · chains A, B, C, E
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D, H, 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	370	0.73	0.84	72	SO4
2	60	0.71	0.97	22	SO4
3	281	0.71	0.85	26	SO4
4	358	0.71	0.83	27	SO4
5	229	0.70	0.87	26	SO4

Interfaces

18 interfaces between chains.

B–K · 873 Å² buried · 12 hydrogen bonds · protein-protein
E–H · 866 Å² buried · 14 hydrogen bonds · protein-protein
I–L · 866 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 865 Å² buried · 12 hydrogen bonds · protein-protein
G–J · 862 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5YL5 · Crystal structure of dodecameric Dehydroquinate dehydratase from Acinetobacter baumannii… · the same entry in another collection · chain L against L, 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 A3M692
Elsewhere: RCSB PDB 5YL5 · PDBe 5YL5 · UniProt A3M692

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