MolNFT v1 · #153844 · protein
Crystal structure of nanobody
6JRI: “Crystal structure of nanobody”. X-ray diffraction, 7 pockets (best druggability 0.66). MolNFT v1 #153844 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JRI
- Type
- protein
- Length
- 989 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Nanobody | protein | 129 | 9% helix, 53% strand | — |
| A | Nanobody | protein | 125 | 10% helix, 55% strand | — |
| D | Nanobody | protein | 127 | 7% helix, 52% strand | — |
| E | Nanobody | protein | 119 | 10% helix, 54% strand | — |
| F | Nanobody | protein | 120 | 10% helix, 53% strand | — |
| G | Nanobody | protein | 120 | 8% helix, 57% strand | — |
| H | Nanobody | protein | 120 | 10% helix, 53% strand | — |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.66 | 0.75 | 68 | empty |
| 2 | 335 | 0.61 | 0.78 | 33 | empty |
| 3 | 390 | 0.60 | 0.76 | 44 | empty |
| 4 | 312 | 0.58 | 0.77 | 35 | empty |
| 5 | 240 | 0.57 | 0.78 | 29 | empty |
Interfaces
12 interfaces between chains.
- C–F · 799 Ų buried · 12 hydrogen bonds · protein-protein
- C–G · 583 Ų buried · 14 hydrogen bonds · protein-protein
- B–A · 528 Ų buried · 13 hydrogen bonds · protein-protein
- D–H · 516 Ų buried · 4 hydrogen bonds · protein-protein
- E–H · 451 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6JRI · Crystal structure of Nanobody · the same entry in another collection · chain B against B, 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 6JRI · PDBe 6JRI
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