Research workbench
Structure of intrinsic factor-cobalamin bound to its receptor cubilin
Analyse Structure of intrinsic factor-cobalamin bound to its receptor cubilin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KQ4
- Type
- protein
- Length
- 2,526 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gastric intrinsic factor; Cubilin
- UniProt
- P27352, O60494
- Ligands
- B12, NAG, MAN, BMA, CA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Gastric intrinsic factor | protein | 385 | 47% helix, 13% strand | P27352 |
| B, D, F | Cubilin | protein | 457 | 0% helix, 40% strand | O60494 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 3 copies · chains A, C, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, B, C, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, B, C, D, E, F
- BMA · beta-D-mannopyranose · sugar · 6 copies
- CA · Calcium ion · metal · 12 copies · chains B, A, D, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.76 | 0.82 | 57 | empty |
| 2 | 801 | 0.73 | 0.78 | 68 | B12 |
| 3 | 759 | 0.72 | 0.78 | 70 | B12 |
| 4 | 920 | 0.71 | 0.75 | 70 | B12 |
| 5 | 64 | 0.63 | 0.92 | 16 | empty |
Interfaces
7 interfaces between chains.
- C–E · 1133 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 929 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 927 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 925 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 214 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 3KQ4 · Structure of Intrinsic Factor-Cobalamin bound to its receptor Cubilin · the same entry in another collection · chain C against C, TM-score 1.00
- P27352 · AlphaFold monomer V2.0 prediction for cobalamin binding intrinsic factor (P27352) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P27352
- Every structure of UniProt O60494
- Elsewhere: RCSB PDB 3KQ4 · PDBe 3KQ4 · UniProt P27352 · UniProt O60494
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