MolNFT v1 · #124388 · protein
Zmpb metallopeptidase in complex with an O-glycopeptide (A2,6- sialylated core-3 pentapeptide).
5KDS · ALPHA2,6-sialylated core-3 pentapeptide: “Zmpb metallopeptidase in complex with an O-glycopeptide (A2,6- sialylated core-3 pentapeptide).”. X-ray diffraction, 4 ligands (A2G, NAG, SIA), 6 pockets (best druggability 0.50). MolNFT v1…
- PDB
- 5KDS
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALPHA2,6-sialylated core-3 pentapeptide; F5/8 type C domain protein
- UniProt
- A0A0H2YN38
- Ligands
- A2G, NAG, SIA, ZN
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | ALPHA2,6-sialylated core-3 pentapeptide | protein | 5 | 0% helix, 0% strand | — |
| A | F5/8 type C domain protein | protein | 511 | 34% helix, 22% strand | A0A0H2YN38 |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains G, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains G, A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- ZN · Zinc ion · metal · chains G, A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
- TLA · L(+)-tartaric acid · additive · chains G, A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.50 | 0.76 | 35 | EDO |
| 2 | 97 | 0.43 | 0.78 | 17 | empty |
| 3 | 50 | 0.33 | 0.78 | 16 | EDO |
| 4 | 73 | 0.32 | 0.75 | 12 | empty |
| 5 | 80 | 0.32 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- G–A · 197 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (O-glycosylation).
Compared structures
- 5KDS · ZmpB metallopeptidase in complex with an O-glycopeptide (a2,6-sialylated core-3… · the same entry in another collection · chain G against G, 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 A0A0H2YN38
- Elsewhere: RCSB PDB 5KDS · PDBe 5KDS · UniProt A0A0H2YN38
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