MolNFT v1 · #29517 · protein
Recognition of peptide ligands by signalling protein from porcine mammary gland (spp-40): crystal structure of the complex of spp-40 with a peptide TRP-pro-TRP at 2.45A resolution
1ZB5 · Signal processing protein: “Recognition of peptide ligands by signalling protein from porcine mammary gland (spp-40): crystal structure…”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.58). MolNFT v1 #29517 on…
- PDB
- 1ZB5
- Type
- protein
- Length
- 367 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal processing protein; Peptide TRP-pro-TRP
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal processing protein | protein | 361 | 37% helix, 24% strand | — |
| B, C | Peptide TRP-pro-TRP | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.58 | 0.77 | 34 | empty |
| 2 | 226 | 0.57 | 0.79 | 34 | empty |
| 3 | 51 | 0.28 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–C · 103 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 90 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1ZB5 · Recognition of peptide ligands by signalling protein from porcine mammary gland (SPP-40)… · 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 1ZB5 · PDBe 1ZB5
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