MolNFT v1 · #124390 · protein
Zmpb metallopeptidase in complex with A2,6-sialyl T-antigen
5KDU · F5/8 type C domain protein: “Zmpb metallopeptidase in complex with A2,6-sialyl T-antigen”. X-ray diffraction, 5 ligands (SER, A2G, GAL), 4 pockets (best druggability 0.51). MolNFT v1 #124390 on GenesisL1: 3D structure, binding sites…
- PDB
- 5KDU
- Type
- protein
- Length
- 512 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F5/8 type C domain protein
- UniProt
- A0A0H2YN38
- Ligands
- SER, A2G, GAL, SIA, ZN
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | F5/8 type C domain protein | protein | 512 | 33% helix, 22% strand | A0A0H2YN38 |
Ligands and binding sites
- SER · Serine · ligand · chains A
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.51 | 0.77 | 31 | EDO |
| 2 | 56 | 0.31 | 0.76 | 14 | EDO |
| 3 | 50 | 0.29 | 0.76 | 11 | empty |
| 4 | 58 | 0.29 | 0.75 | 14 | empty |
Compared structures
- 5KDU · ZmpB metallopeptidase in complex with a2,6-Sialyl T-antigen · 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 A0A0H2YN38
- Elsewhere: RCSB PDB 5KDU · PDBe 5KDU · UniProt A0A0H2YN38
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