MolNFT v1 · #179552 · protein
DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scfv)
7K93 · Non-structural protein 1: “DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scfv)”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.77). MolNFT v1 #179552 on GenesisL1: 3D structure…
- PDB
- 7K93
- Type
- protein
- Length
- 2,244 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 1; 2B7 single chain Fab variable region
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- D0EPS0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 1 (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 327 | 17% helix, 32% strand | D0EPS0 |
| B | Non-structural protein 1 (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 328 | 17% helix, 34% strand | D0EPS0 |
| C | Non-structural protein 1 (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 335 | 17% helix, 33% strand | D0EPS0 |
| D | Non-structural protein 1 (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 325 | 17% helix, 35% strand | D0EPS0 |
| E | 2B7 single chain Fab variable region | protein | 233 | 4% helix, 48% strand | — |
| G, I, K | 2B7 single chain Fab variable region | protein | 232 | 4% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.77 | 0.79 | 110 | empty |
| 2 | 519 | 0.75 | 0.83 | 45 | empty |
| 3 | 117 | 0.74 | 0.94 | 24 | empty |
| 4 | 571 | 0.72 | 0.80 | 40 | empty |
| 5 | 127 | 0.71 | 0.92 | 29 | empty |
Interfaces
13 interfaces between chains.
- C–D · 2826 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2817 Ų buried · 47 hydrogen bonds · protein-protein
- A–E · 707 Ų buried · 7 hydrogen bonds · protein-protein
- B–G · 694 Ų buried · 9 hydrogen bonds · protein-protein
- D–K · 682 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7K93 · DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scFv) · 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 D0EPS0
- Elsewhere: RCSB PDB 7K93 · PDBe 7K93 · UniProt D0EPS0
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