MolNFT v1 · #125095 · protein

Structure of SEC23 and TANGO1 complex

5KYN · Protein transport protein SEC23A: “Structure of SEC23 and TANGO1 complex”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.70). MolNFT v1 #125095 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KYN
Type: protein
Length: 1,452 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein transport protein SEC23A; Melanoma inhibitory activity protein 3
UniProt: Q15436
Ligands: ZN
Pockets: 20 · best druggability 0.70

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	730	32% helix, 22% strand	Q15436
B	Protein transport protein SEC23A	protein	719	34% helix, 22% strand	Q15436
C	Melanoma inhibitory activity protein 3	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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	500	0.70	0.80	63	empty
2	206	0.70	0.87	30	empty
3	348	0.69	0.82	47	empty
4	232	0.67	0.84	33	empty
5	398	0.65	0.79	57	empty

Interfaces

1 interface between chains.

B–C · 210 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5KYN · Structure of Sec23 and TANGO1 complex · 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 B 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
Elsewhere: RCSB PDB 5KYN · PDBe 5KYN · UniProt Q15436

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