MolNFT v1 · #18065 · protein

Crystal structure of the copii coat subunit, SEC24, complexed with a peptide from the snare protein SED5 (yeast syntaxin-5)

1PD0 · Protein transport protein SEC24: “Crystal structure of the copii coat subunit, SEC24, complexed with a peptide from the snare protein SED5…”. X-ray diffraction, 1 ligand (ZN), 13 pockets (best druggability 0.85). MolNFT v1 #18065 on…

PDB: 1PD0
Type: protein
Length: 744 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 integral membrane protein…
UniProt: P40482, Q01590
Ligands: ZN
Pockets: 13 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein transport protein SEC24	protein	734	33% helix, 22% strand	P40482
B	Copii-binding peptide of the integral membrane protein SED5	protein	10	0% helix, 10% strand	Q01590

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

13 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	344	0.85	0.95	48	empty
2	331	0.61	0.78	40	empty
3	281	0.56	0.77	31	empty
4	146	0.47	0.78	20	empty
5	54	0.45	0.84	20	empty

Interfaces

1 interface between chains.

A–B · 667 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1PD0 · 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
Q01590 · AlphaFold monomer V2.0 prediction for integral membrane protein SED5 (Q01590) · a predicted model of the same protein · chain B against A, TM-score 0.33

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 Q01590
Elsewhere: RCSB PDB 1PD0 · PDBe 1PD0 · UniProt P40482 · UniProt Q01590

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