MolNFT v1 · #137525 · protein
CH1/CKAPPA Fab based on matuzumab
5VR9 · CH1/CKAPPA Fab heavy chain: “CH1/CKAPPA Fab based on matuzumab”. X-ray diffraction, 13 pockets (best druggability 0.64). MolNFT v1 #137525 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VR9
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CH1/CKAPPA Fab heavy chain; CH1/CKAPPA Fab light chain
- UniProt
- Q6GMX6, Q7Z3Y4
- Pockets
- 13 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CH1/CKAPPA Fab heavy chain | protein | 222 | 7% helix, 50% strand | Q6GMX6 |
| B | CH1/CKAPPA Fab light chain | protein | 210 | 6% helix, 52% strand | Q7Z3Y4 |
| H | CH1/CKAPPA Fab heavy chain | protein | 224 | 7% helix, 51% strand | Q6GMX6 |
| L | CH1/CKAPPA Fab light chain | protein | 212 | 6% helix, 54% strand | Q7Z3Y4 |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.64 | 0.77 | 54 | empty |
| 2 | 458 | 0.60 | 0.75 | 40 | empty |
| 3 | 325 | 0.59 | 0.77 | 47 | empty |
| 4 | 275 | 0.55 | 0.76 | 37 | empty |
| 5 | 200 | 0.52 | 0.77 | 28 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1815 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1738 Ų buried · 15 hydrogen bonds · protein-protein
- B–L · 822 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5VR9 · CH1/Ckappa Fab based on Matuzumab · 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
- Every structure of UniProt Q6GMX6
- Every structure of UniProt Q7Z3Y4
- Elsewhere: RCSB PDB 5VR9 · PDBe 5VR9 · UniProt Q6GMX6 · UniProt Q7Z3Y4
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