MolNFT v1 · #6483 · protein

N-acetylneuraminate lyase in complex with hydroxypyruvate

1FDY: “N-acetylneuraminate lyase in complex with hydroxypyruvate”. X-ray diffraction, 1 ligand (3PY), 13 pockets (best druggability 0.75). MolNFT v1 #6483 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1FDY
Type: protein
Length: 1,165 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: 3PY
Pockets: 13 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	N-acetylneuraminate lyase (EC 4.1.3.3)	protein	292	53% helix, 13% strand	P0A6L4
B, C, D	N-acetylneuraminate lyase (EC 4.1.3.3)	protein	291	53% helix, 14% strand	P0A6L4

Ligands and binding sites

3PY · 3-hydroxypyruvic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	201	0.75	0.90	26	empty
2	188	0.74	0.90	26	empty
3	345	0.68	0.82	34	3PY
4	441	0.68	0.80	50	3PY
5	337	0.68	0.81	32	3PY

Interfaces

4 interfaces between chains.

B–C · 1195 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 1195 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 1039 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 1025 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

1FDY · N-acetylneuraminate lyase in complex with hydroxypyruvate · the same entry in another collection · chain A against A, TM-score 1.00
P0A6L4 · AlphaFold monomer V2.0 prediction for N-acetylneuraminate lyase (P0A6L4) · a predicted model of the same protein · chain B 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 1FDY · PDBe 1FDY · UniProt P0A6L4

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