Research workbench
Crystal structure of ptpdelta IG1-FN1 in complex with SALM5 lrr-ig
Analyse Crystal structure of ptpdelta IG1-FN1 in complex with SALM5 lrr-ig in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XWT
- Type
- protein
- Length
- 1,447 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, Q96NI6
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase delta (EC 3.1.3.48) | protein | 382 | 1% helix, 51% strand | Q64487 |
| B | Leucine-rich repeat and fibronectin type-III domain- containing protein 5 | protein | 345 | 6% helix, 25% strand | Q96NI6 |
| C | Receptor-type tyrosine-protein phosphatase delta (EC 3.1.3.48) | protein | 374 | 1% helix, 51% strand | Q64487 |
| D | Leucine-rich repeat and fibronectin type-III domain- containing protein 5 | protein | 346 | 6% helix, 25% strand | Q96NI6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.73 | 0.78 | 93 | empty |
| 2 | 57 | 0.71 | 0.97 | 24 | empty |
| 3 | 698 | 0.70 | 0.77 | 79 | empty |
| 4 | 459 | 0.70 | 0.81 | 54 | empty |
| 5 | 526 | 0.67 | 0.78 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1450 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1426 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1220 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5XWT · Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig · the same entry in another collection · chain D against D, TM-score 1.00
- Q96NI6 · 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 C against A, TM-score 0.60
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 Q96NI6
- Elsewhere: RCSB PDB 5XWT · PDBe 5XWT · UniProt Q64487 · UniProt Q96NI6
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