MolNFT v1 · #31931 · protein
Structure of cobalamin-complexed bovine transcobalamin in monoclinic crystal form
2BB6 · Transcobalamin II: “Structure of cobalamin-complexed bovine transcobalamin in monoclinic crystal form”. X-ray diffraction, 2 ligands (B12, CL), 20 pockets (best druggability 0.80). MolNFT v1 #31931 on GenesisL1: 3D structure…
- PDB
- 2BB6
- Type
- protein
- Length
- 1,656 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcobalamin II
- UniProt
- Q9XSC9
- Ligands
- B12, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transcobalamin II | protein | 414 | 46% helix, 12% strand | Q9XSC9 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.80 | 0.82 | 63 | CL, B12 |
| 2 | 1077 | 0.80 | 0.81 | 81 | CL, B12 |
| 3 | 999 | 0.80 | 0.81 | 61 | CL, B12 |
| 4 | 1199 | 0.78 | 0.80 | 77 | CL, B12 |
| 5 | 167 | 0.61 | 0.83 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 680 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 436 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 171 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 158 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2BB6 · Structure of Cobalamin-complexed Bovine Transcobalamin in Monoclinic Crystal Form · the same entry in another collection · chain C against C, 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 0.97
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 2BB6 · PDBe 2BB6 · UniProt Q9XSC9
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