MolNFT v1 · #46129 · protein
Crystal structure of a C-terminal phosphatase domain of rattus norvegicus ortholog of human protein tyrosine phosphatase, receptor type, D (ptprd)
2NV5 · Ptprd, phosphatase: “Crystal structure of a C-terminal phosphatase domain of rattus norvegicus ortholog of human protein tyrosine…”. X-ray diffraction, 9 pockets (best druggability 0.79). MolNFT v1 #46129 on GenesisL1: 3D structure…
- PDB
- 2NV5
- Type
- protein
- Length
- 849 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ptprd, phosphatase
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ptprd, phosphatase | protein | 283 | 36% helix, 24% strand | — |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.79 | 0.80 | 104 | empty |
| 2 | 248 | 0.55 | 0.77 | 26 | empty |
| 3 | 163 | 0.52 | 0.79 | 25 | empty |
| 4 | 122 | 0.41 | 0.75 | 23 | empty |
| 5 | 55 | 0.39 | 0.80 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1089 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 102 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2NV5 · Crystal structure of a C-terminal phosphatase domain of Rattus norvegicus ortholog of… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2NV5 · PDBe 2NV5
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