Research workbench
TC:CD320 in complex with nanobody tc-NB11
Analyse TC:CD320 in complex with nanobody tc-NB11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QBE
- Type
- protein
- Length
- 1,201 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcobalamin-2; CD320 antigen; Anti-transcobalamin-2 nanobody tc-NB11
- UniProt
- P20062, Q9NPF0
- Ligands
- CNC, CA
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcobalamin-2 | protein | 394 | 48% helix, 13% strand | P20062 |
| B | CD320 antigen | protein | 80 | 14% helix, 15% strand | Q9NPF0 |
| C | Transcobalamin-2 | protein | 395 | 48% helix, 13% strand | P20062 |
| D | CD320 antigen | protein | 86 | 14% helix, 14% strand | Q9NPF0 |
| E, F | Anti-transcobalamin-2 nanobody tc-NB11 | protein | 123 | 2% helix, 43% strand | — |
Ligands and binding sites
- CNC · Cyanocobalamin · ligand · 2 copies · chains A, C
- CA · Calcium ion · metal · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.81 | 0.83 | 101 | empty |
| 2 | 990 | 0.80 | 0.81 | 67 | CNC |
| 3 | 1038 | 0.79 | 0.81 | 84 | CNC |
| 4 | 157 | 0.57 | 0.82 | 24 | empty |
| 5 | 258 | 0.56 | 0.77 | 33 | empty |
Interfaces
8 interfaces between chains.
- C–F · 978 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 905 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 894 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 883 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 548 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide (disulfide).
Compared structures
- 7QBE · TC:CD320 in complex with nanobody TC-Nb11 · the same entry in another collection · chain F against F, TM-score 1.00
- P20062 · AlphaFold monomer V2.0 prediction for transcobalamin-2 (P20062) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q9NPF0 · AlphaFold monomer V2.0 prediction for CD320 antigen (Q9NPF0) · a predicted model of the same protein · chain B against A, TM-score 0.47
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 P20062
- Every structure of UniProt Q9NPF0
- Elsewhere: RCSB PDB 7QBE · PDBe 7QBE · UniProt P20062 · UniProt Q9NPF0
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