MolNFT v1 · #185731 · protein
TC:CD320 in complex with nanobody tc-NB34
7QBF · Transcobalamin-2: “TC:CD320 in complex with nanobody tc-NB34”. X-ray diffraction, 3 ligands (CNC, CA, IOD), 9 pockets (best druggability 0.78). MolNFT v1 #185731 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7QBF
- Type
- protein
- Length
- 612 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcobalamin-2; CD320 antigen; Anti-transcobalamin-2 nanobody tc-NB34
- UniProt
- P20062, Q9NPF0
- Ligands
- CNC, CA, IOD
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcobalamin-2 | protein | 409 | 46% helix, 13% strand | P20062 |
| C | CD320 antigen | protein | 78 | 15% helix, 15% strand | Q9NPF0 |
| B | Anti-transcobalamin-2 nanobody tc-NB34 | protein | 125 | 10% helix, 44% strand | — |
Ligands and binding sites
- CNC · Cyanocobalamin · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A, C
- IOD · Iodide ion · ion · 16 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 27 copies · chains A, C, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.78 | 0.80 | 87 | IOD, EDO, CNC |
| 2 | 81 | 0.59 | 0.88 | 22 | EDO, IOD |
| 3 | 69 | 0.57 | 0.88 | 19 | IOD, EDO |
| 4 | 109 | 0.47 | 0.80 | 20 | EDO |
| 5 | 63 | 0.43 | 0.82 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1074 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1068 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7QBF · TC:CD320 in complex with nanobody TC-Nb34 · the same entry in another collection · chain A against A, TM-score 1.00
- P20062 · AlphaFold monomer V2.0 prediction for transcobalamin-2 (P20062) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q9NPF0 · AlphaFold monomer V2.0 prediction for CD320 antigen (Q9NPF0) · a predicted model of the same protein · chain C against A, TM-score 0.49
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 7QBF · PDBe 7QBF · UniProt P20062 · UniProt Q9NPF0
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