Research workbench
Crystallographic analysis of upper axial ligand substitutions in cobalamin bound to transcobalamin
Analyse Crystallographic analysis of upper axial ligand substitutions in cobalamin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V3N
- Type
- protein
- Length
- 405 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcobalamin-2
- UniProt
- Q9XSC9
- Ligands
- B12, CL, CYN
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcobalamin-2 | protein | 405 | 47% helix, 13% strand | Q9XSC9 |
Ligands and binding sites
- B12 · Cobalamin · ligand · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- CYN · Cyanide ion · ion
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.72 | 0.76 | 55 | B12, CYN, CL |
| 2 | 171 | 0.50 | 0.78 | 29 | empty |
| 3 | 95 | 0.48 | 0.81 | 24 | empty |
| 4 | 98 | 0.39 | 0.76 | 23 | empty |
| 5 | 85 | 0.32 | 0.73 | 16 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2V3N · Crystallographic analysis of upper axial ligand substitutions in cobalamin bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XSC9 · AlphaFold monomer V2.0 prediction for transcobalamin-2 (Q9XSC9) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9XSC9
- Elsewhere: RCSB PDB 2V3N · PDBe 2V3N · UniProt Q9XSC9
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