Research workbench
Crystal structures of human SALM5 in complex with human ptpdelta
Analyse Crystal structures of human SALM5 in complex with human ptpdelta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XNP
- Type
- protein
- Length
- 1,304 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich repeat and fibronectin type-III domain- containing protein 5; Receptor-type…
- EC
- 3.1.3.48
- UniProt
- Q96NI6, P23468
- Ligands
- NAG, CA, NA, CL, SO4
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Leucine-rich repeat and fibronectin type-III domain- containing protein 5 | protein | 361 | 8% helix, 27% strand | Q96NI6 |
| D, E | Receptor-type tyrosine-protein phosphatase delta (EC 3.1.3.48) | protein | 291 | 0% helix, 52% strand | P23468 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, D, E
- CA · Calcium ion · metal · 12 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 12 copies · chains A, B, D, E
- SO4 · Sulfate ion · ion · 4 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.70 | 0.83 | 45 | NA, CL |
| 2 | 564 | 0.64 | 0.75 | 71 | empty |
| 3 | 508 | 0.63 | 0.76 | 66 | empty |
| 4 | 453 | 0.62 | 0.76 | 49 | empty |
| 5 | 412 | 0.61 | 0.76 | 35 | empty |
Interfaces
3 interfaces between chains.
- B–E · 1403 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1397 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1107 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5XNP · Crystal structures of human SALM5 in complex with human PTPdelta · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.99
- P23468 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase delta… · a predicted model of the same protein · chain D against A, TM-score 0.78
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 Q96NI6
- Every structure of UniProt P23468
- Elsewhere: RCSB PDB 5XNP · PDBe 5XNP · UniProt Q96NI6 · UniProt P23468
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