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L-kdo aldolase

Analyse L-kdo aldolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LCX
Type: protein
Length: 1,164 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-acetylneuraminate lyase
EC: 4.1.3.3
UniProt: P0A6L4
Ligands: SO4
Pockets: 14 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	N-acetylneuraminate lyase (EC 4.1.3.3)	protein	291	54% helix, 13% strand	P0A6L4

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	764	0.76	0.80	90	SO4
2	197	0.74	0.90	28	empty
3	196	0.73	0.89	24	empty
4	307	0.67	0.82	38	SO4
5	324	0.67	0.81	42	SO4

Interfaces

4 interfaces between chains.

A–D · 1229 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1208 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1080 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 1056 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

3LCX · L-KDO aldolase · 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 P0A6L4
Elsewhere: RCSB PDB 3LCX · PDBe 3LCX · UniProt P0A6L4

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