MolNFT v1 · #141574 · protein
Crystal structure of xenopus embryonic epidermal lectin in complex with samarium ions
5ZC0: “Crystal structure of xenopus embryonic epidermal lectin in complex with samarium ions”. X-ray diffraction, 2 ligands (SM, CA), 12 pockets (best druggability 0.86). MolNFT v1 #141574 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ZC0
- Type
- protein
- Length
- 1,686 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xenopus embryonic epidermal lectin
- UniProt
- Q5PPM0
- Ligands
- SM, CA
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Xenopus embryonic epidermal lectin | protein | 281 | 20% helix, 26% strand | Q5PPM0 |
Ligands and binding sites
- SM · Samarium (III) ion · metal · 27 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.86 | 0.88 | 129 | empty |
| 2 | 951 | 0.86 | 0.87 | 110 | empty |
| 3 | 76 | 0.54 | 0.86 | 21 | empty |
| 4 | 89 | 0.42 | 0.78 | 15 | empty |
| 5 | 84 | 0.41 | 0.78 | 15 | empty |
Interfaces
9 interfaces between chains.
- D–F · 898 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 897 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 888 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 879 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 867 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 5ZC0 · Crystal structure of Xenopus embryonic epidermal lectin in complex with Samarium ions · the same entry in another collection · chain C against C, TM-score 1.00
- Q5PPM0 · AlphaFold monomer V2.0 prediction for intelectin-1 (Q5PPM0) · a predicted model of the same protein · 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 Q5PPM0
- Elsewhere: RCSB PDB 5ZC0 · PDBe 5ZC0 · UniProt Q5PPM0
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