MolNFT v1 · #112649 · protein
E88 deletion mutant of CD320 in complex with TC2
4ZRQ · Transcobalamin-2: “E88 deletion mutant of CD320 in complex with TC2”. X-ray diffraction, 2 ligands (CNC, CA), 15 pockets (best druggability 0.78). MolNFT v1 #112649 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZRQ
- Type
- protein
- Length
- 950 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcobalamin-2; CD320 antigen
- UniProt
- P20062, Q9NPF0
- Ligands
- CNC, CA
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcobalamin-2 | protein | 400 | 47% helix, 13% strand | P20062 |
| B | Transcobalamin-2 | protein | 399 | 47% helix, 13% strand | P20062 |
| C | CD320 antigen | protein | 76 | 8% helix, 8% strand | Q9NPF0 |
| D | CD320 antigen | protein | 75 | 8% helix, 11% strand | Q9NPF0 |
Ligands and binding sites
- CNC · Cyanocobalamin · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.78 | 0.85 | 75 | GOL |
| 2 | 872 | 0.76 | 0.79 | 58 | CNC |
| 3 | 1009 | 0.74 | 0.77 | 71 | CNC, GOL |
| 4 | 772 | 0.70 | 0.76 | 85 | empty |
| 5 | 235 | 0.64 | 0.83 | 39 | empty |
Interfaces
6 interfaces between chains.
- B–D · 913 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 828 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 563 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 231 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 225 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 4ZRQ · E88 deletion mutant of CD320 in complex with TC2 · the same entry in another collection · chain D against D, TM-score 1.00
- P20062 · AlphaFold monomer V2.0 prediction for transcobalamin-2 (P20062) · a predicted model of the same protein · chain B 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 0.51
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 4ZRQ · PDBe 4ZRQ · UniProt P20062 · UniProt Q9NPF0
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