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Crystal structure of a novel N-acetylneuraminic acid lyase from corynebacterium glutamicum

Analyse Crystal structure of a novel N-acetylneuraminic acid lyase from corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C54
Type: protein
Length: 2,473 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydrodipicolinate SYNTHASE/N-acetylneuraminate lyase
EC: 4.1.3.3
UniProt: Q8NMD2
Pockets: 18 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, F, H	Dihydrodipicolinate SYNTHASE/N-acetylneuraminate lyase (EC 4.1.3.3)	protein	310	50% helix, 10% strand	Q8NMD2
D	Dihydrodipicolinate SYNTHASE/N-acetylneuraminate lyase (EC 4.1.3.3)	protein	308	50% helix, 10% strand	Q8NMD2
E	Dihydrodipicolinate SYNTHASE/N-acetylneuraminate lyase (EC 4.1.3.3)	protein	308	50% helix, 10% strand	Q8NMD2
G	Dihydrodipicolinate SYNTHASE/N-acetylneuraminate lyase (EC 4.1.3.3)	protein	307	51% helix, 10% strand	Q8NMD2

Ligands and binding sites

GOL · Glycerol · additive · 10 copies · chains A, B, C, D, E, F, G, H

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

Pockets

18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	537	0.71	0.80	63	GOL
2	500	0.70	0.80	54	GOL
3	484	0.70	0.80	55	GOL
4	475	0.70	0.80	54	GOL
5	471	0.70	0.80	55	GOL

Interfaces

10 interfaces between chains.

C–D · 1972 Å² buried · 28 hydrogen bonds · protein-protein
G–H · 1965 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 1965 Å² buried · 29 hydrogen bonds · protein-protein
E–F · 1956 Å² buried · 30 hydrogen bonds · protein-protein
A–D · 931 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5C54 · Crystal structure of a novel N-acetylneuraminic acid lyase from Corynebacterium glutamicum · 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 Q8NMD2
Elsewhere: RCSB PDB 5C54 · PDBe 5C54 · UniProt Q8NMD2

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