MolNFT v1 · #52952 · protein
Crystal structure of the complex between human hedgehog-interacting protein hip and desert hedgehog without calcium
2WG3 · Desert hedgehog protein N-product: “Crystal structure of the complex between human hedgehog-interacting protein hip and desert hedgehog without…”. X-ray diffraction, 4 ligands (NAG, ZN, CL), 16 pockets (best druggability 0.80).…
- PDB
- 2WG3
- Type
- protein
- Length
- 1,120 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Desert hedgehog protein N-product; Hedgehog-interacting protein
- UniProt
- O43323, Q96QV1
- Ligands
- NAG, ZN, CL, PO4
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Desert hedgehog protein N-product | protein | 155 | 25% helix, 17% strand | O43323 |
| B | Desert hedgehog protein N-product | protein | 150 | 24% helix, 21% strand | O43323 |
| C | Hedgehog-interacting protein | protein | 406 | 6% helix, 39% strand | Q96QV1 |
| D | Hedgehog-interacting protein | protein | 409 | 5% helix, 41% strand | Q96QV1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, D
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.80 | 0.83 | 70 | CL |
| 2 | 779 | 0.79 | 0.83 | 69 | PO4 |
| 3 | 171 | 0.55 | 0.80 | 28 | empty |
| 4 | 159 | 0.54 | 0.80 | 33 | empty |
| 5 | 186 | 0.54 | 0.78 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–C · 976 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 784 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 249 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 239 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2WG3 · Crystal structure of the complex between human hedgehog-interacting protein HIP and… · the same entry in another collection · chain D against D, TM-score 1.00
- Q96QV1 · AlphaFold monomer V2.0 prediction for hedgehog-interacting protein (Q96QV1) · a predicted model of the same protein · chain C against A, TM-score 0.99
- O43323 · AlphaFold monomer V2.0 prediction for desert hedgehog protein (O43323) · a predicted model of the same protein · chain B 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 O43323
- Every structure of UniProt Q96QV1
- Elsewhere: RCSB PDB 2WG3 · PDBe 2WG3 · UniProt O43323 · UniProt Q96QV1
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