Research workbench
Structure of phage TP901-1 rbp (ORF49) in complex with nanobody 11.
Analyse Structure of phage TP901-1 rbp (ORF49) in complex with nanobody 11. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IOS
- Type
- protein
- Length
- 861 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bpp; Llama nanobody 11
- UniProt
- Q9G096
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Bpp | protein | 100 | 3% helix, 49% strand | Q9G096 |
| B, C | Bpp | protein | 99 | 3% helix, 49% strand | Q9G096 |
| D | Llama nanobody 11 | protein | 113 | 3% helix, 50% strand | — |
| E | Llama nanobody 11 | protein | 118 | 3% helix, 50% strand | — |
| F | Llama nanobody 11 | protein | 115 | 3% helix, 50% strand | — |
| G | Llama nanobody 11 | protein | 117 | 3% helix, 49% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.74 | 0.98 | 19 | empty |
| 2 | 290 | 0.66 | 0.82 | 37 | empty |
| 3 | 248 | 0.62 | 0.81 | 38 | empty |
| 4 | 223 | 0.61 | 0.82 | 30 | empty |
| 5 | 364 | 0.54 | 0.73 | 49 | empty |
Interfaces
12 interfaces between chains.
- B–C · 819 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 782 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 532 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 529 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4IOS · Structure of phage TP901-1 RBP (ORF49) in complex with nanobody 11. · 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 Q9G096
- Elsewhere: RCSB PDB 4IOS · PDBe 4IOS · UniProt Q9G096
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