MolNFT v1 · #35181 · protein
Crystal structure of cert start domain in complex with C16- ceramide (P212121)
2E3O · Lipid-transfer protein cert: “Crystal structure of cert start domain in complex with C16- ceramide (P212121)”. X-ray diffraction, 1 ligand (16C), 2 pockets (best druggability 0.85). MolNFT v1 #35181 on GenesisL1: 3D structure…
- PDB
- 2E3O
- Type
- protein
- Length
- 231 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipid-transfer protein cert
- UniProt
- Q53YV2
- Ligands
- 16C
- Pockets
- 2 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipid-transfer protein cert | protein | 231 | 26% helix, 39% strand | Q53YV2 |
Ligands and binding sites
- 16C · N-((E,2S,3R)-1,3-dihydroxyoctadec-4-en-2-yl)palmitamide · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.85 | 0.92 | 46 | 16C |
| 2 | 90 | 0.36 | 0.75 | 15 | empty |
Compared structures
- 2E3O · Crystal structure of CERT START domain in complex with C16-ceramide (P212121) · 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 Q53YV2
- Elsewhere: RCSB PDB 2E3O · PDBe 2E3O · UniProt Q53YV2
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