MolNFT v1 · #35184 · protein

Crystal structure of cert start domain in complex with C18- ceramide (P1)

2E3R · Lipid-transfer protein cert: “Crystal structure of cert start domain in complex with C18- ceramide (P1)”. X-ray diffraction, 1 ligand (18C), 3 pockets (best druggability 0.85). MolNFT v1 #35184 on GenesisL1: 3D structure, binding…

PDB: 2E3R
Type: protein
Length: 453 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipid-transfer protein cert
UniProt: Q53YV2
Ligands: 18C
Pockets: 3 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lipid-transfer protein cert	protein	227	26% helix, 38% strand	Q53YV2
B	Lipid-transfer protein cert	protein	226	27% helix, 40% strand	Q53YV2

Ligands and binding sites

18C · N-((E,2S,3R)-1,3-dihydroxyoctadec-4-en-2-yl)stearamide · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	520	0.85	0.91	51	18C
2	512	0.85	0.91	46	18C
3	586	0.60	0.73	56	empty

Interfaces

1 interface between chains.

A–B · 428 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2E3R · Crystal structure of CERT START domain in complex with C18-ceramide (P1) · 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 2E3R · PDBe 2E3R · UniProt Q53YV2

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