MolNFT v1 · #185729 · protein
TC:CD320 in complex with nanobody tc-NB26
7QBD · Transcobalamin-2: “TC:CD320 in complex with nanobody tc-NB26”. X-ray diffraction, 2 ligands (CNC, CA), 17 pockets (best druggability 0.80). MolNFT v1 #185729 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7QBD
- Type
- protein
- Length
- 1,068 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcobalamin-2; CD320 antigen; Antitranscobalamin-nanobody tc-NB26
- UniProt
- P20062, Q9NPF0
- Ligands
- CNC, CA
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transcobalamin-2 | protein | 400 | 47% helix, 13% strand | P20062 |
| C | CD320 antigen | protein | 76 | 18% helix, 16% strand | Q9NPF0 |
| D | CD320 antigen | protein | 78 | 18% helix, 18% strand | Q9NPF0 |
| E | Antitranscobalamin-nanobody tc-NB26 | protein | 114 | 0% helix, 38% strand | — |
Ligands and binding sites
- CNC · Cyanocobalamin · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.80 | 0.82 | 102 | empty |
| 2 | 1048 | 0.74 | 0.77 | 72 | CNC, CA |
| 3 | 1029 | 0.74 | 0.77 | 70 | CNC, CA |
| 4 | 132 | 0.58 | 0.84 | 25 | empty |
| 5 | 63 | 0.58 | 0.89 | 21 | empty |
Interfaces
7 interfaces between chains.
- B–D · 885 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 885 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 615 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 568 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 150 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 7QBD · TC:CD320 in complex with nanobody TC-Nb26 · the same entry in another collection · chain E against E, 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 0.99
- Q9NPF0 · AlphaFold monomer V2.0 prediction for CD320 antigen (Q9NPF0) · a predicted model of the same protein · chain C 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 7QBD · PDBe 7QBD · UniProt P20062 · UniProt Q9NPF0
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