MolNFT v1 · #118254 · protein
Crystal structure of the human Fab VRC38.01, an HIV-1 V1V2-directed neutralizing antibody isolated from donor N90
5EWI · VRC38.01 heavy chain: “Crystal structure of the human Fab VRC38.01, an HIV-1 V1V2-directed neutralizing antibody isolated from donor…”. X-ray diffraction, 4 pockets (best druggability 0.60). MolNFT v1 #118254 on GenesisL1: 3D…
- PDB
- 5EWI
- Type
- protein
- Length
- 438 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC38.01 heavy chain; VRC38.01 light chain
- UniProt
- Q6N089, P01834
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | VRC38.01 heavy chain | protein | 221 | 7% helix, 52% strand | Q6N089 |
| L | VRC38.01 light chain | protein | 217 | 6% helix, 51% strand | P01834 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.60 | 0.74 | 58 | empty |
| 2 | 54 | 0.58 | 0.91 | 19 | empty |
| 3 | 189 | 0.46 | 0.74 | 33 | empty |
| 4 | 77 | 0.31 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- H–L · 2080 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5EWI · Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing Antibody… · the same entry in another collection · chain H against H, TM-score 1.00
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain L against A, TM-score 0.48
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 Q6N089
- Every structure of UniProt P01834
- Elsewhere: RCSB PDB 5EWI · PDBe 5EWI · UniProt Q6N089 · UniProt P01834
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