Research workbench
Anti-sudan ebolavirus nucleoprotein single domain antibody sudan B (sb) complexed with sudan ebolavirus nucleoprotein C-terminal domain 634-738
Analyse Anti-sudan ebolavirus nucleoprotein single domain antibody sudan B (sb)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U52
- Type
- protein
- Length
- 422 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-sudan ebolavirus nucleoprotein single domain antibody sudan B (sb); Nucleoprotein
- UniProt
- Q9QP77
- Ligands
- CL
- Pockets
- 7 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Anti-sudan ebolavirus nucleoprotein single domain antibody sudan B (sb) | protein | 119 | 5% helix, 52% strand | — |
| B | Nucleoprotein | protein | 88 | 47% helix, 14% strand | Q9QP77 |
| D | Nucleoprotein | protein | 96 | 50% helix, 17% strand | Q9QP77 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.53 | 0.87 | 29 | empty |
| 2 | 131 | 0.44 | 0.77 | 23 | empty |
| 3 | 78 | 0.42 | 0.80 | 20 | empty |
| 4 | 108 | 0.42 | 0.77 | 20 | empty |
| 5 | 72 | 0.39 | 0.79 | 18 | CL |
Interfaces
6 interfaces between chains.
- B–C · 808 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 771 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 669 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 657 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 78 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6U52 · Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB) Complexed with… · 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 Q9QP77
- Elsewhere: RCSB PDB 6U52 · PDBe 6U52 · UniProt Q9QP77
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