MolNFT v1 · #51374 · protein
Complex structure of human IGF2R domains 11-13 bound to igf-II
2V5P · Cation-independent mannose-6-phosphate receptor: “Complex structure of human IGF2R domains 11-13 bound to igf-II”. X-ray diffraction, 2 ligands (NAG, BMA), 15 pockets (best druggability 0.74). MolNFT v1 #51374 on GenesisL1: 3D…
- PDB
- 2V5P
- Type
- protein
- Length
- 1,028 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cation-independent mannose-6-phosphate receptor; Insulin-like growth factor II
- UniProt
- P11717, P01344
- Ligands
- NAG, BMA
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cation-independent mannose-6-phosphate receptor | protein | 466 | 4% helix, 39% strand | P11717 |
| C, D | Insulin-like growth factor II | protein | 48 | 40% helix, 4% strand | P01344 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
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 | 961 | 0.74 | 0.78 | 90 | empty |
| 2 | 805 | 0.72 | 0.77 | 69 | empty |
| 3 | 147 | 0.63 | 0.85 | 21 | empty |
| 4 | 110 | 0.62 | 0.87 | 28 | empty |
| 5 | 194 | 0.59 | 0.81 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 820 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 797 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 106 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 2V5P · Complex structure of human IGF2R domains 11-13 bound to igf-II · the same entry in another collection · chain A against A, TM-score 1.00
- P01344 · AlphaFold monomer V2.0 prediction for insulin-like growth factor II (P01344) · a predicted model of the same protein · chain C against A, TM-score 0.75
- P11717 · AlphaFold monomer V2.0 prediction for cation-independent mannose-6-phosphate receptor… · a predicted model of the same protein · chain A against A, TM-score 0.47
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 P11717
- Every structure of UniProt P01344
- Elsewhere: RCSB PDB 2V5P · PDBe 2V5P · UniProt P11717 · UniProt P01344
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