MolNFT v1 · #185732 · protein
TC:CD320 in complex with nanobody tc-NB4
7QBG · Transcobalamin-2: “TC:CD320 in complex with nanobody tc-NB4”. X-ray diffraction, 2 ligands (CNC, CA), 14 pockets (best druggability 0.81). MolNFT v1 #185732 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7QBG
- Type
- protein
- Length
- 1,181 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcobalamin-2; CD320 antigen; Anti-TC:CD320 nanobody tc-NB4
- UniProt
- P20062, Q9NPF0
- Ligands
- CNC, CA
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcobalamin-2 | protein | 381 | 49% helix, 13% strand | P20062 |
| B | CD320 antigen | protein | 85 | 11% helix, 14% strand | Q9NPF0 |
| C | Transcobalamin-2 | protein | 388 | 47% helix, 12% strand | P20062 |
| D | CD320 antigen | protein | 81 | 11% helix, 15% strand | Q9NPF0 |
| E | Anti-TC:CD320 nanobody tc-NB4 | protein | 125 | 5% helix, 48% strand | — |
| G | Anti-TC:CD320 nanobody tc-NB4 | protein | 121 | 2% helix, 44% strand | — |
Ligands and binding sites
- CNC · Cyanocobalamin · ligand · 2 copies · chains A, C
- CA · Calcium ion · metal · 6 copies · chains B, C, D, A, E, G
- GOL · Glycerol · additive · 3 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.81 | 0.82 | 87 | CNC |
| 2 | 1181 | 0.80 | 0.81 | 88 | CNC |
| 3 | 534 | 0.76 | 0.83 | 51 | empty |
| 4 | 217 | 0.71 | 0.87 | 43 | GOL |
| 5 | 652 | 0.68 | 0.76 | 66 | empty |
Interfaces
10 interfaces between chains.
- B–C · 998 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 940 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 903 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 755 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 573 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 7QBG · TC:CD320 in complex with nanobody TC-Nb4 · the same entry in another collection · chain G against G, 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 D against A, TM-score 0.48
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 7QBG · PDBe 7QBG · UniProt P20062 · UniProt Q9NPF0
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