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R106G KDO8PS without substrates

Analyse R106G KDO8PS without substrates in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1T99
Type: protein
Length: 511 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-dehydro-3-deoxyphosphooctonate aldolase
EC: 2.5.1.55
UniProt: O66496
Ligands: CD, PO4
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55)	protein	256	41% helix, 20% strand	O66496
B	2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55)	protein	255	43% helix, 21% strand	O66496

Ligands and binding sites

CD · Cadmium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	417	0.79	0.88	45	PO4
2	413	0.78	0.87	49	PO4
3	89	0.55	0.85	34	empty
4	109	0.44	0.78	21	empty

Interfaces

1 interface between chains.

A–B · 1700 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

1T99 · r106g kdo8ps without substrates · 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 O66496
Elsewhere: RCSB PDB 1T99 · PDBe 1T99 · UniProt O66496

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