MolNFT v1 · #146230 · protein
Crystal structure of vhh R330
6DBE · Nanobody vhh R303: “Crystal structure of vhh R330”. X-ray diffraction, 2 pockets (best druggability 0.79). MolNFT v1 #146230 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DBE
- Type
- protein
- Length
- 228 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody vhh R303
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody vhh R303 | protein | 115 | 3% helix, 56% strand | — |
| B | Nanobody vhh R303 | protein | 113 | 5% helix, 56% strand | — |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.79 | 0.85 | 64 | EPE |
| 2 | 54 | 0.32 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 519 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6DBE · Crystal Structure of VHH R330 · 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 6DBE · PDBe 6DBE
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