MolNFT v1 · #140002 · protein
Crystal structure of ptpdelta IG1-IG3 in complex with SALM2 lrr-ig
5XWU · Receptor-type tyrosine-protein phosphatase delta: “Crystal structure of ptpdelta IG1-IG3 in complex with SALM2 lrr-ig”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.64). MolNFT v1 #140002 on GenesisL1: 3D…
- PDB
- 5XWU
- Type
- protein
- Length
- 1,270 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-type tyrosine-protein phosphatase delta; Leucine-rich repeat and fibronectin…
- EC
- 3.1.3.48
- UniProt
- Q64487, Q2WF71
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase delta (EC 3.1.3.48) | protein | 293 | 2% helix, 55% strand | Q64487 |
| B | Leucine-rich repeat and fibronectin type III domain- containing protein 1 | protein | 343 | 7% helix, 26% strand | Q2WF71 |
| C | Receptor-type tyrosine-protein phosphatase delta (EC 3.1.3.48) | protein | 294 | 2% helix, 54% strand | Q64487 |
| D | Leucine-rich repeat and fibronectin type III domain- containing protein 1 | protein | 340 | 7% helix, 24% strand | Q2WF71 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, D, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.64 | 0.81 | 55 | empty |
| 2 | 226 | 0.64 | 0.82 | 28 | empty |
| 3 | 400 | 0.63 | 0.77 | 47 | empty |
| 4 | 210 | 0.61 | 0.82 | 28 | empty |
| 5 | 91 | 0.61 | 0.88 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1359 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1338 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1249 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 5XWU · Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig · the same entry in another collection · chain D against D, TM-score 1.00
- Q2WF71 · AlphaFold monomer V2.0 prediction for leucine-rich repeat and fibronectin type III… · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q64487 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase delta… · a predicted model of the same protein · chain A against A, TM-score 0.77
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 Q64487
- Every structure of UniProt Q2WF71
- Elsewhere: RCSB PDB 5XWU · PDBe 5XWU · UniProt Q64487 · UniProt Q2WF71
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