MolNFT v1 · #18063 · protein

Crystal structure of the copii coat subunit, SEC24, complexed with a peptide from the snare protein BET1

1PCX · Protein transport protein SEC24: “Crystal structure of the copii coat subunit, SEC24, complexed with a peptide from the snare protein BET1”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.79). MolNFT v1 #18063 on…

PDB: 1PCX
Type: protein
Length: 753 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein transport protein SEC24; Copii-binding peptide of the protein transport protein…
UniProt: P40482, P22804
Ligands: ZN
Pockets: 12 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein transport protein SEC24	protein	745	33% helix, 21% strand	P40482
B	Copii-binding peptide of the protein transport protein BET1	protein	8	63% helix, 0% strand	P22804

Ligands and binding sites

ZN · Zinc ion · metal · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	568	0.79	0.85	66	empty
2	344	0.61	0.77	39	empty
3	188	0.54	0.78	21	empty
4	89	0.43	0.79	21	empty
5	147	0.42	0.74	16	empty

Interfaces

1 interface between chains.

A–B · 511 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

1PCX · Crystal structure of the COPII coat subunit, Sec24, complexed with a peptide from the… · the same entry in another collection · chain A against A, TM-score 1.00
P40482 · AlphaFold monomer V2.0 prediction for protein transport protein SEC24 (P40482) · a predicted model of the same protein · chain A against A, TM-score 1.00
P22804 · AlphaFold monomer V2.0 prediction for protein transport protein BET1 (P22804) · a predicted model of the same protein · chain B against A, TM-score 0.77

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 P40482
Every structure of UniProt P22804
Elsewhere: RCSB PDB 1PCX · PDBe 1PCX · UniProt P40482 · UniProt P22804

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