Research workbench
Crystal structure of VRC03 ghvglv antigen-binding fragment.
Analyse Crystal structure of VRC03 ghvglv antigen-binding fragment. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JOF
- Type
- protein
- Length
- 1,726 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC03 ghv heavy chain; VRC03 glv light chain
- Ligands
- SO4
- Pockets
- 19 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, E | VRC03 ghv heavy chain | protein | 224 | 8% helix, 52% strand | — |
| L | VRC03 glv light chain | protein | 211 | 8% helix, 50% strand | — |
| A | VRC03 ghv heavy chain | protein | 220 | 4% helix, 48% strand | — |
| B, D, F | VRC03 glv light chain | protein | 210 | 7% helix, 54% strand | — |
| C | VRC03 ghv heavy chain | protein | 217 | 6% helix, 49% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.61 | 0.75 | 51 | empty |
| 2 | 397 | 0.60 | 0.76 | 47 | empty |
| 3 | 184 | 0.53 | 0.79 | 28 | empty |
| 4 | 328 | 0.53 | 0.74 | 41 | empty |
| 5 | 304 | 0.52 | 0.74 | 46 | empty |
Interfaces
11 interfaces between chains.
- H–L · 1960 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1915 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1701 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1667 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 373 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5JOF · Crystal structure of VRC03 gHVgLV antigen-binding fragment. · 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 5JOF · PDBe 5JOF
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