MolNFT v1 · #190777 · protein
Crystal structure of the AM0627 (E326A) inactive mutant in complex with psgl-1-like bis-T glycopeptide and ZN2+
7YX8 · Peptidase M60 domain-containing protein: “Crystal structure of the AM0627 (E326A) inactive mutant in complex with psgl-1-like bis-T glycopeptide and…”. X-ray diffraction, 3 ligands (A2G, GAL, ZN), 10 pockets (best druggability…
- PDB
- 7YX8
- Type
- protein
- Length
- 893 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase M60 domain-containing protein; Psgl-1-like bis-T glycopeptide
- UniProt
- B2UPI7
- Ligands
- A2G, GAL, ZN
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidase M60 domain-containing protein | protein | 440 | 41% helix, 21% strand | B2UPI7 |
| B | Peptidase M60 domain-containing protein | protein | 438 | 41% helix, 22% strand | B2UPI7 |
| F | Psgl-1-like bis-T glycopeptide | protein | 7 | 0% helix, 14% strand | — |
| H | Psgl-1-like bis-T glycopeptide | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains B, F, A, H
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains B, F, A, H
- ZN · Zinc ion · metal · 2 copies · chains A, H, B, F
- GOL · Glycerol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.67 | 0.75 | 74 | A2G, GAL |
| 2 | 362 | 0.59 | 0.77 | 32 | empty |
| 3 | 440 | 0.56 | 0.73 | 50 | empty |
| 4 | 245 | 0.51 | 0.75 | 38 | A2G, GAL |
| 5 | 120 | 0.41 | 0.76 | 18 | GOL |
Interfaces
5 interfaces between chains.
- A–B · 539 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 513 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 494 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 145 Ų buried · 3 hydrogen bonds · protein-protein
- B–H · 104 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (O-glycosylation).
Compared structures
- 7YX8 · Crystal structure of the AM0627 (E326A) inactive mutant in complex with PSGL-1-like bis-T… · 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
- Every structure of UniProt B2UPI7
- Elsewhere: RCSB PDB 7YX8 · PDBe 7YX8 · UniProt B2UPI7
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