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Crystal structure of SEC23A/SEC24A/SEC22 complexed with EMP24 sorting motif

Analyse Crystal structure of SEC23A/SEC24A/SEC22 complexed with EMP24 sorting motif in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VNE
Type: protein
Length: 1,575 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein transport protein SEC23A; Protein transport protein SEC24A; Vesicle-trafficking…
UniProt: Q15436, O95486, O08547
Ligands: ZN
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein transport protein SEC23A	protein	708	33% helix, 23% strand	Q15436
B	Protein transport protein SEC24A	protein	729	29% helix, 21% strand	O95486
C	Vesicle-trafficking protein SEC22B	protein	135	36% helix, 27% strand	O08547
D	EMP24	protein	3	0% helix, 0% 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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	982	0.83	0.84	120	empty
2	732	0.80	0.84	78	empty
3	408	0.73	0.83	53	empty
4	393	0.68	0.81	50	empty
5	265	0.68	0.84	29	empty

Interfaces

4 interfaces between chains.

A–B · 953 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 685 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 328 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 255 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5VNE · Crystal structure of Sec23a/Sec24a/Sec22 complexed with Emp24 sorting motif · 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 1.00
O95486 · AlphaFold monomer V2.0 prediction for protein transport protein SEC24A (O95486) · a predicted model of the same protein · chain B against A, TM-score 0.98
O08547 · AlphaFold monomer V2.0 prediction for vesicle-trafficking protein SEC22B (O08547) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 O95486
Every structure of UniProt O08547
Elsewhere: RCSB PDB 5VNE · PDBe 5VNE · UniProt Q15436 · UniProt O95486 · UniProt O08547

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