Research workbench

Cryo-EM structure of saccharomyces cerevisiae er membrane protein complex bound to Fab-DH4 in lipid nanodiscs

Analyse Cryo-EM structure of saccharomyces cerevisiae er membrane protein complex bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KRA
Type: protein
Length: 2,164 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Er membrane protein complex subunit 1; Er membrane protein complex subunit 2; Er membrane…
UniProt: P25574, P47133, P36039, P53073, P40540, Q12431, P39543, Q12025
Ligands: X3P, NAG
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 12 distinct chains · 28% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Er membrane protein complex subunit 1	protein	694	10% helix, 37% strand	P25574
B	Er membrane protein complex subunit 2	protein	290	74% helix, 0% strand	P47133
C	Er membrane protein complex subunit 3	protein	188	61% helix, 2% strand	P36039
D	Er membrane protein complex subunit 4	protein	68	44% helix, 0% strand	P53073
E	Er membrane protein complex subunit 5	protein	129	58% helix, 1% strand	P40540
F	Er membrane protein complex subunit 6	protein	95	63% helix, 1% strand	Q12431
G	Protein SOP4	protein	151	0% helix, 34% strand	P39543
H	Endoplasmic reticulum membrane protein complex subunit 10	protein	125	0% helix, 53% strand	Q12025
I	Fab DH4 heavy chain	protein	170	0% helix, 34% strand	—
J	Fab DH4 light chain	protein	209	2% helix, 46% strand	—
M	Unassigned helix	protein	21	90% helix, 0% strand	—
N	Unassigned helix	protein	24	92% helix, 0% strand	—

Ligands and binding sites

X3P · [(2~{R})-1-octanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propan-2-yl] nonanoate · ligand · chains C, D, F
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, G

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	322	0.80	0.90	51	empty
2	1083	0.75	0.78	99	empty
3	541	0.73	0.81	62	empty
4	449	0.73	0.83	62	empty
5	884	0.71	0.75	70	empty

Interfaces

23 interfaces between chains.

B–E · 2287 Å² buried · 18 hydrogen bonds · protein-protein
A–G · 1892 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 1831 Å² buried · 6 hydrogen bonds · protein-protein
A–H · 1639 Å² buried · 21 hydrogen bonds · protein-protein
I–J · 1560 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

7KRA · Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein complex bound to… · the same entry in another collection · chain N against N, TM-score 1.00

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 P25574
Every structure of UniProt P47133
Every structure of UniProt P36039
Every structure of UniProt P53073
Every structure of UniProt P40540
Every structure of UniProt Q12431
Every structure of UniProt P39543
Every structure of UniProt Q12025
Elsewhere: RCSB PDB 7KRA · PDBe 7KRA · UniProt P25574 · UniProt P47133 · UniProt P36039 · UniProt P53073 · UniProt P40540 · UniProt Q12431 · UniProt P39543 · UniProt Q12025

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.