Research workbench
Crystal structure of GL12A21 Fab in complex with anti-idiotypic IV12 Fab
Analyse Crystal structure of GL12A21 Fab in complex with anti-idiotypic IV12 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VRQ
- Type
- protein
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IV12 Fab heavy chain; IV12 Fab light chain; GL12A21 Fab heavy chain; GL12A21 Fab light…
- Ligands
- K, CL
- Pockets
- 9 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | IV12 Fab heavy chain | protein | 215 | 9% helix, 54% strand | — |
| L | IV12 Fab light chain | protein | 212 | 5% helix, 50% strand | — |
| A | GL12A21 Fab heavy chain | protein | 222 | 9% helix, 50% strand | — |
| B | GL12A21 Fab light chain | protein | 207 | 7% helix, 49% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains L, A, B
- CL · Chloride ion · ion · 4 copies · chains A, B, L
- EDO · 1,2-ethanediol · additive · 5 copies · chains H, A, L, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains H, L, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.54 | 0.74 | 42 | empty |
| 2 | 186 | 0.53 | 0.78 | 27 | EDO |
| 3 | 159 | 0.47 | 0.76 | 31 | empty |
| 4 | 169 | 0.44 | 0.75 | 35 | PEG |
| 5 | 143 | 0.37 | 0.72 | 20 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1743 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1706 Ų buried · 12 hydrogen bonds · protein-protein
- H–A · 576 Ų buried · 10 hydrogen bonds · protein-protein
- L–A · 308 Ų buried · 5 hydrogen bonds · protein-protein
- H–B · 131 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6VRQ · Crystal structure of gl12A21 Fab in complex with anti-idiotypic iv12 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 6VRQ · PDBe 6VRQ
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.