MolNFT v1 · #52276 · protein

Structure of the catalytic domain of streptococcus pneumoniae sialidase nana

2VVZ · Sialidase a: “Structure of the catalytic domain of streptococcus pneumoniae sialidase nana”. X-ray diffraction, 2 ligands (DAN, CL), 7 pockets (best druggability 0.74). MolNFT v1 #52276 on GenesisL1: 3D structure, binding sites and…

PDB: 2VVZ
Type: protein
Length: 940 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sialidase a
EC: 3.2.1.18
UniProt: P62575
Ligands: DAN, CL
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Sialidase a (EC 3.2.1.18)	protein	470	2% helix, 41% strand	P62575

Ligands and binding sites

DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · chains A

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

Pockets

7 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	1151	0.74	0.77	101	empty
2	295	0.62	0.80	36	empty
3	300	0.60	0.79	27	empty
4	123	0.58	0.84	21	DAN
5	116	0.55	0.83	21	DAN

Interfaces

1 interface between chains.

A–B · 1296 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

2VVZ · Structure of the catalytic domain of Streptococcus pneumoniae sialidase NanA · the same entry in another collection · chain A against A, TM-score 1.00
P62575 · AlphaFold monomer V2.0 prediction for sialidase a (P62575) · a predicted model of the same protein · chain A 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 P62575
Elsewhere: RCSB PDB 2VVZ · PDBe 2VVZ · UniProt P62575

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