Research workbench

Crystal structure of human nal at a resolution of 1.6 ångström

Analyse Crystal structure of human nal at a resolution of 1.6 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ARH
Type: protein
Length: 1,204 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: Q9BXD5
Pockets: 17 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	N-acetylneuraminate lyase (EC 4.1.3.3)	protein	300	51% helix, 13% strand	Q9BXD5
B	N-acetylneuraminate lyase (EC 4.1.3.3)	protein	303	50% helix, 13% strand	Q9BXD5
D	N-acetylneuraminate lyase (EC 4.1.3.3)	protein	301	50% helix, 13% strand	Q9BXD5

Ligands and binding sites

ACT · Acetate ion · additive · 8 copies · chains A, D, B, C

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

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.74	0.99	23	empty
2	62	0.74	0.99	21	empty
3	466	0.67	0.78	36	ACT
4	486	0.67	0.78	35	ACT
5	514	0.65	0.77	40	ACT

Interfaces

4 interfaces between chains.

A–D · 1700 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1671 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1346 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1343 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

6ARH · Crystal structure of Human NAL at a resolution of 1.6 Angstrom · the same entry in another collection · chain A against A, TM-score 1.00
Q9BXD5 · AlphaFold monomer V2.0 prediction for N-acetylneuraminate lyase (Q9BXD5) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 Q9BXD5
Elsewhere: RCSB PDB 6ARH · PDBe 6ARH · UniProt Q9BXD5

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