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Crystal structure of dehydroquinate dehydratase with tris induced oligomerisation at 1.907 ångström resolution

Analyse Crystal structure of dehydroquinate dehydratase with tris induced… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YHM
Type: protein
Length: 1,742 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-dehydroquinate dehydratase
UniProt: A3M692
Ligands: SO4
Pockets: 20 · best druggability 0.72

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	protein	145	48% helix, 16% strand	A3M692
K	3-dehydroquinate dehydratase	protein	147	46% helix, 16% strand	A3M692

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, E, F, G, D, H, L, I, J, K

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	400	0.72	0.83	32	SO4
2	364	0.71	0.83	32	SO4
3	413	0.71	0.82	35	SO4
4	406	0.71	0.82	29	SO4
5	318	0.71	0.84	31	SO4

Interfaces

18 interfaces between chains.

I–L · 882 Å² buried · 13 hydrogen bonds · protein-protein
E–H · 881 Å² buried · 12 hydrogen bonds · protein-protein
B–K · 877 Å² buried · 13 hydrogen bonds · protein-protein
G–J · 872 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 869 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5YHM · Crystal structure of dehydroquinate dehydratase with tris induced oligomerisation at… · 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 5YHM · PDBe 5YHM · UniProt A3M692

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