MolNFT v1 · #157570 · protein

Cryo-EM structure of the yeast sec complex

6N3Q · Protein transport protein SEC61: “Cryo-EM structure of the yeast sec complex”. Electron microscopy, 14 pockets (best druggability 0.85). MolNFT v1 #157570 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6N3Q
Type: protein
Length: 1,290 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein transport protein SEC61; Protein transport protein SSS1; Protein transport…
UniProt: P32915, P35179, P52870, P14906, P33754, P39742
Pockets: 14 · best druggability 0.85

Structure

electron microscopy · 6 distinct chains · 60% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein transport protein SEC61	protein	391	64% helix, 5% strand	P32915
C	Protein transport protein SSS1	protein	55	84% helix, 0% strand	P35179
B	Protein transport protein SBH1	protein	32	88% helix, 3% strand	P52870
D	Protein translocation protein SEC63	protein	487	43% helix, 12% strand	P14906
E	Translocation protein SEC66	protein	135	81% helix, 0% strand	P33754
F	Translocation protein SEC72	protein	190	71% helix, 1% strand	P39742

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1130	0.85	0.86	108	empty
2	651	0.73	0.80	59	empty
3	482	0.65	0.76	51	empty
4	222	0.63	0.82	36	empty
5	243	0.61	0.80	36	empty

Interfaces

10 interfaces between chains.

E–F · 2180 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1879 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 1616 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 1164 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 861 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6N3Q · Cryo-EM structure of the yeast Sec complex · the same entry in another collection · chain F against F, TM-score 1.00
P32915 · AlphaFold monomer V2.0 prediction for protein transport protein SEC61 (P32915) · a predicted model of the same protein · chain A against A, TM-score 0.92
P14906 · AlphaFold monomer V2.0 prediction for protein translocation protein SEC63 (P14906) · a predicted model of the same protein · chain D against A, TM-score 0.91
P52870 · AlphaFold monomer V2.0 prediction for protein transport protein SBH1 (P52870) · a predicted model of the same protein · chain B against A, TM-score 0.86
P33754 · AlphaFold monomer V2.0 prediction for translocation protein SEC66 (P33754) · a predicted model of the same protein · chain E against A, TM-score 0.81
P39742 · AlphaFold monomer V2.0 prediction for translocation protein SEC72 (P39742) · a predicted model of the same protein · chain F against A, TM-score 0.80
P35179 · AlphaFold monomer V2.0 prediction for protein transport protein SSS1 (P35179) · a predicted model of the same protein · chain C against A, TM-score 0.65

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 P32915
Every structure of UniProt P35179
Every structure of UniProt P52870
Every structure of UniProt P14906
Every structure of UniProt P33754
Every structure of UniProt P39742
Elsewhere: RCSB PDB 6N3Q · PDBe 6N3Q · UniProt P32915 · UniProt P35179 · UniProt P52870 · UniProt P14906 · UniProt P33754 · UniProt P39742

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