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Crystal structure of an abridged form of the mature ectodomain of the human receptor-type protein tyrosine phosphatase ICA512/IA-2 at pH 4.5
Analyse Crystal structure of an abridged form of the mature ectodomain of the human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NP5
- Type
- protein
- Length
- 353 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-type tyrosine-protein phosphatase-like N
- UniProt
- Q16849
- Ligands
- CA
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase-like N | protein | 87 | 40% helix, 30% strand | Q16849 |
| B, D | Receptor-type tyrosine-protein phosphatase-like N | protein | 89 | 39% helix, 31% strand | Q16849 |
| C | Receptor-type tyrosine-protein phosphatase-like N | protein | 88 | 40% helix, 31% strand | Q16849 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.82 | 0.83 | 93 | empty |
| 2 | 58 | 0.44 | 0.83 | 16 | empty |
| 3 | 63 | 0.26 | 0.72 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 487 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 433 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 417 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 397 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3NP5 · Crystal structure of an abridged form of the mature ectodomain of the human receptor-type… · the same entry in another collection · chain A against A, TM-score 1.00
- Q16849 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase-like N… · a predicted model of the same protein · chain A 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 Q16849
- Elsewhere: RCSB PDB 3NP5 · PDBe 3NP5 · UniProt Q16849
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