MolNFT v1 · #150023 · protein
Variable heavy - variable light domain and Fab-arm crossmabs with charged residue exchanges
6GHG · Fab heavy chain: “Variable heavy - variable light domain and Fab-arm crossmabs with charged residue exchanges”. X-ray diffraction, 1 ligand (NA), 15 pockets (best druggability 0.62). MolNFT v1 #150023 on GenesisL1: 3D structure…
- PDB
- 6GHG
- Type
- protein
- Length
- 857 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain
- Ligands
- NA
- Pockets
- 15 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab heavy chain | protein | 217 | 8% helix, 52% strand | — |
| B | Fab light chain | protein | 214 | 7% helix, 50% strand | — |
| H | Fab heavy chain | protein | 211 | 9% helix, 51% strand | — |
| L | Fab light chain | protein | 215 | 7% helix, 53% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, L
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, B, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.62 | 0.86 | 26 | empty |
| 2 | 278 | 0.57 | 0.77 | 35 | empty |
| 3 | 115 | 0.55 | 0.84 | 22 | NA |
| 4 | 271 | 0.49 | 0.73 | 39 | P6G |
| 5 | 162 | 0.49 | 0.77 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1695 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1587 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 571 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6GHG · Variable heavy - variable light domain and Fab-arm CrossMabs with charged residue… · the same entry in another collection · chain A against A, 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 6GHG · PDBe 6GHG
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