MolNFT v1 · #138230 · protein
Crystal structure of the broadly neutralizing influenza a antibody vrc 315 04-1D02 Fab.
5WCD · VRC315 04-1D02 Fab heavy chain: “Crystal structure of the broadly neutralizing influenza a antibody vrc 315 04-1D02 Fab.”. X-ray diffraction, 2 ligands (SO4, PO4), 3 pockets (best druggability 0.64). MolNFT v1 #138230 on GenesisL1…
- PDB
- 5WCD
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC315 04-1D02 Fab heavy chain; VRC315 04-1D02 Fab light chain
- Ligands
- SO4, PO4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | VRC315 04-1D02 Fab heavy chain | protein | 217 | 9% helix, 51% strand | — |
| L | VRC315 04-1D02 Fab light chain | protein | 212 | 7% helix, 51% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.64 | 0.74 | 56 | empty |
| 2 | 52 | 0.41 | 0.82 | 19 | SO4 |
| 3 | 61 | 0.30 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- H–L · 1809 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5WCD · Crystal structure of the broadly neutralizing Influenza A antibody VRC 315 04-1D02 Fab. · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 5WCD · PDBe 5WCD
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