MolNFT v1 · #137177 · protein
Crystal structure of the human Fab VRC38.01, an HIV-1 V1V2-directed neutralizing antibody isolated from donor N90, bound to a scaffolded wito V1V2 domain
5VGJ · 1FD6-V1V2-wito: “Crystal structure of the human Fab VRC38.01, an HIV-1 V1V2-directed neutralizing antibody isolated from donor…”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 6 pockets (best druggability 0.57). MolNFT v1 #137177 on…
- PDB
- 5VGJ
- Type
- protein
- Length
- 560 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1FD6-V1V2-wito; VRC38.01 Fab heavy chain; VRC38.01 Fab light chain
- Ligands
- MAN, NAG, BMA
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | 1FD6-V1V2-wito | protein | 119 | 12% helix, 43% strand | — |
| H | VRC38.01 Fab heavy chain | protein | 224 | 6% helix, 52% strand | — |
| L | VRC38.01 Fab light chain | protein | 217 | 6% helix, 52% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains H, L, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains G, H, L
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.57 | 0.92 | 21 | empty |
| 2 | 437 | 0.56 | 0.73 | 49 | empty |
| 3 | 93 | 0.38 | 0.76 | 28 | empty |
| 4 | 112 | 0.38 | 0.74 | 22 | empty |
| 5 | 92 | 0.35 | 0.75 | 14 | MAN |
Interfaces
3 interfaces between chains.
- H–L · 2134 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 421 Ų buried · 6 hydrogen bonds · protein-protein
- G–L · 118 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5VGJ · Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing Antibody… · the same entry in another collection · chain G against G, 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 5VGJ · PDBe 5VGJ
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