MolNFT v1 · #112648 · protein
TC:CD320
4ZRP · Transcobalamin-2: “TC:CD320”. X-ray diffraction, 2 ligands (CNC, CA), 14 pockets (best druggability 0.79). MolNFT v1 #112648 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZRP
- Type
- protein
- Length
- 956 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
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcobalamin-2 | protein | 400 | 47% helix, 13% strand | P20062 |
| B | Transcobalamin-2 | protein | 399 | 46% helix, 13% strand | P20062 |
| C | CD320 antigen | protein | 78 | 19% helix, 15% strand | Q9NPF0 |
| D | CD320 antigen | protein | 79 | 15% helix, 15% strand | Q9NPF0 |
Ligands and binding sites
- CNC · Cyanocobalamin · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, C, B, D
- GOL · Glycerol · additive · 6 copies · chains A, B, D, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.79 | 0.81 | 121 | GOL |
| 2 | 1182 | 0.75 | 0.77 | 87 | CNC, CA, GOL |
| 3 | 1065 | 0.74 | 0.77 | 67 | CNC |
| 4 | 671 | 0.67 | 0.76 | 65 | empty |
| 5 | 159 | 0.61 | 0.84 | 29 | GOL |
Interfaces
6 interfaces between chains.
- A–C · 894 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 892 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 569 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 224 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 223 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 4ZRP · TC:CD320 · the same entry in another collection · chain B against B, 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 D 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 4ZRP · PDBe 4ZRP · UniProt P20062 · UniProt Q9NPF0
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