Research workbench
Structure of rvfv gn and human monoclonal antibody R13
Analyse Structure of rvfv gn and human monoclonal antibody R13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IEA
- Type
- protein
- Length
- 728 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nsmgngc; R13 L chain; R13 H chain
- UniProt
- H9BSP3
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nsmgngc | protein | 300 | 12% helix, 32% strand | H9BSP3 |
| L | R13 L chain | protein | 218 | 7% helix, 50% strand | — |
| H | R13 H chain | protein | 210 | 7% helix, 52% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.59 | 0.74 | 49 | empty |
| 2 | 344 | 0.57 | 0.76 | 39 | GOL |
| 3 | 204 | 0.54 | 0.78 | 34 | empty |
| 4 | 74 | 0.52 | 0.85 | 22 | PEG |
| 5 | 166 | 0.48 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1941 Ų buried · 24 hydrogen bonds · protein-protein
- A–L · 442 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 355 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6IEA · Structure of RVFV Gn and human monoclonal antibody R13 · 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 H9BSP3
- Elsewhere: RCSB PDB 6IEA · PDBe 6IEA · UniProt H9BSP3
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