MolNFT v1 · #116897 · protein
Crystal structure of the BCR Fab fragment from subset #4 case CLL240
5DRX · CLL240 heavy chain (vh and CH1 domains): “Crystal structure of the BCR Fab fragment from subset #4 case CLL240”. X-ray diffraction, 11 pockets (best druggability 0.57). MolNFT v1 #116897 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DRX
- Type
- protein
- Length
- 877 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CLL240 heavy chain (vh and CH1 domains); CLL240 BCR light chain
- Pockets
- 11 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | CLL240 heavy chain (vh and CH1 domains) | protein | 220 | 8% helix, 50% strand | — |
| L | CLL240 BCR light chain | protein | 221 | 5% helix, 50% strand | — |
| A | CLL240 heavy chain (vh and CH1 domains) | protein | 216 | 7% helix, 52% strand | — |
| B | CLL240 BCR light chain | protein | 220 | 5% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains H, L, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.57 | 0.89 | 21 | empty |
| 2 | 294 | 0.53 | 0.75 | 45 | empty |
| 3 | 329 | 0.53 | 0.74 | 45 | empty |
| 4 | 97 | 0.37 | 0.75 | 17 | empty |
| 5 | 85 | 0.35 | 0.74 | 18 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1999 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1894 Ų buried · 20 hydrogen bonds · protein-protein
- H–A · 492 Ų buried · 6 hydrogen bonds · protein-protein
- H–B · 198 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5DRX · Crystal structure of the BCR Fab fragment from subset #4 case CLL240 · 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 5DRX · PDBe 5DRX
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