MolNFT v1 · #15626 · protein

The three-dimensional structure of N-acetylneuraminate lyase from escherichia COLI

1NAL: “The three-dimensional structure of N-acetylneuraminate lyase from escherichia COLI”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.76). MolNFT v1 #15626 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1NAL
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: 12 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1, 2, 3, 4	N-acetylneuraminate lyase (EC 4.1.3.3)	protein	291	52% helix, 13% strand	P0A6L4

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains 1, 2, 3, 4

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

Pockets

12 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	213	0.76	0.90	27	empty
2	219	0.75	0.90	26	empty
3	339	0.69	0.82	39	SO4
4	322	0.68	0.81	34	SO4
5	334	0.67	0.81	35	SO4

Interfaces

4 interfaces between chains.

2–3 · 1207 Å² buried · 14 hydrogen bonds · protein-protein
1–4 · 1204 Å² buried · 14 hydrogen bonds · protein-protein
2–4 · 1037 Å² buried · 16 hydrogen bonds · protein-protein
1–3 · 1017 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1NAL · The three-dimensional structure of N-acetylneuraminate lyase from escherichia COLI · the same entry in another collection · chain 1 against 1, TM-score 1.00
P0A6L4 · AlphaFold monomer V2.0 prediction for N-acetylneuraminate lyase (P0A6L4) · a predicted model of the same protein · chain 1 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 1NAL · PDBe 1NAL · UniProt P0A6L4

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