3LKW: PDB entry 3LKW

Crystal Structure of Dengue Virus 1 NS2B/NS3 protease active site mutant. Determined by X-ray diffraction at 2.0 Å resolution. Released 2 Mar 2010.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Dengue virus type 1 (strain Singapore/S275/1990), Dengue virus type 1 (strain Nauru/West Pac/1974)
Chains: 1
Atoms: 1,694
Mol. weight: 25.38 kDa
Ligands: CD
Released: 2 Mar 2010

Explore 3LKW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3LKW contains 3 α-helices and 20 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	1
β-strand	22-23	2	2
β-strand	32-34	3	3
β-strand	40-42	3	3
α-helix	68-70	3
β-strand	71-79	9	1
β-strand	82-92	11	1
β-strand	95-98	4	1
α-helix	100-103	4
β-strand	108-110	3	1
β-strand	113-115	3	1
β-strand	117-121	5	1
β-strand	126-129	4	1
β-strand	145-149	5	2
β-strand	157-161	5	2
β-strand	164-168	5	4
β-strand	171-176	6	4
β-strand	188-190	3	2
β-strand	196-199	4	2
β-strand	203-205	3	4
β-strand	211-214	4	4
β-strand	216	1	2
α-helix	219-221	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
fusion protein of nonstructural protein 2B and nonstructural protein 3	A	protein	236	Dengue virus type 1 (strain Singapore/S275/1990), Dengue virus type 1 (strain Nauru/West Pac/1974)	P17763 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3LKW_1 fusion protein of nonstructural protein 2B and nonstructural protein 3 (chains A)
GAHMADLSLEKAAEVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLGGGGSGGGG
SGVLWDTPSPGIYRILQRGLLGRSQVGVGVFQEGVFHTMWHVTRGAVLMYQGKRLEPSWA
SVKKDLISYGGGWRFQGSWNAGEEVQVIAVEPGKNPKNVQTAPGTFKTPEGEVGAIALDF
KPGTAGSPIVNREGKIVGLYGNGVVTTSGTYVSAIAQAKASQEGPLPEIEDEVFRK

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	1

Water and common crystallization additives (CL, SO4, GOL) are not listed.

Primary citation

Serotype-specific structural differences in the protease-cofactor complexes of the dengue virus family. Chandramouli, S., Joseph, J.S., Daudenarde, S. et al. J Virol (2010) 84:3059-3067. DOI 10.1128/JVI.02044-09 · PubMed

Other PDB entries of the same protein (UniProt P17763 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LCY 1.6 Å, Crystal structure of HLA-b46 at 1.6 angstrom resolution
4AL8 1.66 Å, Structure of Dengue virus DIII in complex with Fab 2H12
4GSX 1.9 Å, High resolution structure of dengue virus serotype 1 sE containing stem
3L6P 2.2 Å, Crystal Structure of Dengue Virus 1 NS2B/NS3 protease
4GT0 2.57 Å, Structure of dengue virus serotype 1 sE containing stem to residue 421
4OIG 2.69 Å, Dengue Virus Non-structural Protein NS1
8VPR 2.7 Å, Crystal structure of mouse Importin alpha in complex with Dengue 1 NS5 central NLS peptide
5WKF 2.95 Å, D30 TCR in complex with HLA-A*11:01-GTS1
5VIC 3.0 Å, Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII
5WJL 3.15 Å, Crystal Structure of HLA-A*11:01 with GTS1 peptide
7DWT 19.0 Å, Cryo-EM structure of Dengue virus serotype 1 strain WestPac 74 in complex with human…
7DWU 19.0 Å, Cryo-EM structure of Dengue virus serotype 1 strain WestPac 74 in complex with human…

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