MolNFT v1 · #68678 · protein

Crystal structure of B/PERTH neuraminidase D197E mutant in complex with peramivir

3K39: “Crystal structure of B/PERTH neuraminidase D197E mutant in complex with peramivir”. X-ray diffraction, 4 ligands (BCZ, NAG, CA), 20 pockets (best druggability 0.80). MolNFT v1 #68678 on GenesisL1: 3D structure, binding sites and…

PDB: 3K39
Type: protein
Length: 6,224 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuraminidase
EC: 3.2.1.18
UniProt: Q3S340
Ligands: BCZ, NAG, CA, YT3
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	Neuraminidase (EC 3.2.1.18)	protein	389	2% helix, 48% strand	Q3S340

Ligands and binding sites

BCZ · 3-(1-acetylamino-2-ethyl-butyl)-4-guanidino-2-hydroxy-cyclopentanecarboxylic acid · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
YT3 · Yttrium (III) ion · metal · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	935	0.80	0.82	77	BCZ
2	113	0.78	0.98	26	empty
3	111	0.78	0.98	26	empty
4	117	0.78	0.97	26	empty
5	110	0.78	0.97	26	empty

Interfaces

30 interfaces between chains.

I–J · 1988 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1987 Å² buried · 26 hydrogen bonds · protein-protein
A–D · 1986 Å² buried · 25 hydrogen bonds · protein-protein
K–L · 1986 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 1985 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 128 disulfide, 16 glycan (disulfide, N-glycosylation).

Compared structures

3K39 · Crystal Structure of B/Perth Neuraminidase D197E mutant in complex with Peramivir · 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 Q3S340
Elsewhere: RCSB PDB 3K39 · PDBe 3K39 · UniProt Q3S340

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