MolNFT v1 · #62462 · protein

Crystal structure of the mammalian copii-coat protein SEC23/24 bound to the transport signal sequence of membrin

3EG9 · Protein transport protein SEC23A: “Crystal structure of the mammalian copii-coat protein SEC23/24 bound to the transport signal sequence of…”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.77). MolNFT v1 #62462…

PDB: 3EG9
Type: protein
Length: 1,499 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein transport protein SEC23A; SEC24 related gene family, member D; Peptide
UniProt: Q15436, Q8IYI7
Ligands: ZN
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein transport protein SEC23A	protein	726	34% helix, 22% strand	Q15436
B	SEC24 related gene family, member D	protein	767	33% helix, 21% strand	Q8IYI7
C	Peptide	protein	6	0% helix, 50% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	734	0.77	0.81	74	empty
2	488	0.76	0.84	54	empty
3	403	0.73	0.84	48	empty
4	244	0.68	0.84	24	empty
5	362	0.67	0.81	45	empty

Interfaces

2 interfaces between chains.

A–B · 778 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 409 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3EG9 · Crystal structure of the mammalian COPII-coat protein Sec23/24 bound to the transport… · the same entry in another collection · chain A against A, TM-score 1.00
Q15436 · AlphaFold monomer V2.0 prediction for protein transport protein SEC23A (Q15436) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q15436
Every structure of UniProt Q8IYI7
Elsewhere: RCSB PDB 3EG9 · PDBe 3EG9 · UniProt Q15436 · UniProt Q8IYI7

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