MolNFT v1 · #105052 · protein
Crystal structure of ron sema-psi-IPT1 extracellular domains in complex with msp beta-chain
4QT8 · Macrophage-stimulating protein receptor: “Crystal structure of ron sema-psi-IPT1 extracellular domains in complex with msp beta-chain”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.70). MolNFT v1 #105052…
- PDB
- 4QT8
- Type
- protein
- Length
- 1,719 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage-stimulating protein receptor; Hepatocyte growth factor-like protein
- EC
- 2.7.10.1
- UniProt
- Q04912, P26927
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Macrophage-stimulating protein receptor (EC 2.7.10.1) | protein | 629 | 7% helix, 38% strand | Q04912 |
| A | Macrophage-stimulating protein receptor (EC 2.7.10.1) | protein | 628 | 7% helix, 38% strand | Q04912 |
| C | Hepatocyte growth factor-like protein | protein | 231 | 10% helix, 25% strand | P26927 |
| D | Hepatocyte growth factor-like protein | protein | 231 | 10% helix, 25% strand | P26927 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.70 | 0.80 | 32 | empty |
| 2 | 513 | 0.68 | 0.79 | 36 | empty |
| 3 | 409 | 0.68 | 0.80 | 57 | empty |
| 4 | 132 | 0.63 | 0.87 | 36 | empty |
| 5 | 271 | 0.62 | 0.80 | 34 | empty |
Interfaces
4 interfaces between chains.
- A–C · 948 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 918 Ų buried · 13 hydrogen bonds · protein-protein
- B–A · 225 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 167 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4QT8 · Crystal Structure of RON Sema-PSI-IPT1 extracellular domains in complex with MSP… · the same entry in another collection · chain C against C, TM-score 1.00
- Q04912 · AlphaFold monomer V2.0 prediction for macrophage-stimulating protein receptor (Q04912) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P26927 · AlphaFold monomer V2.0 prediction for hepatocyte growth factor-like protein (P26927) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 Q04912
- Every structure of UniProt P26927
- Elsewhere: RCSB PDB 4QT8 · PDBe 4QT8 · UniProt Q04912 · UniProt P26927
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