MolNFT v1 · #117412 · protein
Complex between lactococcal phage TUC2009 rbp head domain and a nanobody (L06)
5E7F · Nanobody L06: “Complex between lactococcal phage TUC2009 rbp head domain and a nanobody (L06)”. X-ray diffraction, 5 pockets (best druggability 0.78). MolNFT v1 #117412 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5E7F
- Type
- protein
- Length
- 764 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody L06; Major structural protein 1
- UniProt
- Q38610
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody L06 | protein | 126 | 8% helix, 47% strand | — |
| B | Nanobody L06 | protein | 125 | 8% helix, 47% strand | — |
| C | Nanobody L06 | protein | 129 | 8% helix, 46% strand | — |
| G, H, I | Major structural protein 1 | protein | 128 | 7% helix, 56% strand | Q38610 |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.78 | 0.81 | 90 | empty |
| 2 | 78 | 0.77 | 0.99 | 18 | empty |
| 3 | 603 | 0.71 | 0.79 | 55 | empty |
| 4 | 95 | 0.53 | 0.84 | 28 | empty |
| 5 | 81 | 0.36 | 0.76 | 16 | empty |
Interfaces
9 interfaces between chains.
- H–I · 998 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 998 Ų buried · 8 hydrogen bonds · protein-protein
- G–I · 986 Ų buried · 9 hydrogen bonds · protein-protein
- C–I · 789 Ų buried · 10 hydrogen bonds · protein-protein
- B–H · 629 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5E7F · Complex between lactococcal phage Tuc2009 RBP head domain and a nanobody (L06) · 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 Q38610
- Elsewhere: RCSB PDB 5E7F · PDBe 5E7F · UniProt Q38610
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