MolNFT v1 · #172792 · protein

Cryo-EM structure of human er membrane protein complex in lipid nanodiscs

7ADO · Er membrane protein complex subunit 1: “Cryo-EM structure of human er membrane protein complex in lipid nanodiscs”. Electron microscopy, 2 ligands (PCW, NAG), 20 pockets (best druggability 0.79). MolNFT v1 #172792 on GenesisL1: 3D…

PDB: 7ADO
Type: protein
Length: 2,085 residues
Chains: 10
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: Q8N766, Q15006, Q9P0I2, Q5J8M3, Q8N4V1, Q9BV81, Q9NPA0, O43402, Q5UCC4
Ligands: PCW, NAG
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 10 distinct chains · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Er membrane protein complex subunit 1	protein	915	10% helix, 38% strand	Q8N766
B	Er membrane protein complex subunit 2	protein	275	75% helix, 0% strand	Q15006
C	Er membrane protein complex subunit 3	protein	203	58% helix, 2% strand	Q9P0I2
D	Er membrane protein complex subunit 4	protein	64	30% helix, 9% strand	Q5J8M3
E	Membrane magnesium transporter 1	protein	97	69% helix, 1% strand	Q8N4V1
F	Er membrane protein complex subunit 6	protein	100	71% helix, 0% strand	Q9BV81
G	Er membrane protein complex subunit 7	protein	97	7% helix, 22% strand	Q9NPA0
H	Er membrane protein complex subunit 8	protein	176	39% helix, 21% strand	O43402
I	Er membrane protein complex subunit 10	protein	142	14% helix, 39% strand	Q5UCC4
K	Unassigned helix	protein	16	88% helix, 0% strand	—

Ligands and binding sites

PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 5 copies · chains A, C, E, F
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, D, G, I

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	737	0.79	0.83	99	empty
2	1108	0.77	0.79	95	empty
3	132	0.77	0.95	21	empty
4	432	0.75	0.85	35	empty
5	134	0.75	0.94	29	empty

Interfaces

20 interfaces between chains.

A–C · 1673 Å² buried · 11 hydrogen bonds · protein-protein
A–I · 1661 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1638 Å² buried · 25 hydrogen bonds · protein-protein
A–G · 1616 Å² buried · 10 hydrogen bonds · protein-protein
B–E · 1549 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).

Compared structures

7ADO · Cryo-EM structure of human ER membrane protein complex in lipid nanodiscs · the same entry in another collection · chain K against K, TM-score 1.00
Q8N766 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 1 (Q8N766) · a predicted model of the same protein · chain A against A, TM-score 0.96
O43402 · AlphaFold monomer V2.0 prediction for er membrane protein complex subunit 8 (O43402) · a predicted model of the same protein · chain H against A, TM-score 0.96

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 Q8N766
Every structure of UniProt Q15006
Every structure of UniProt Q9P0I2
Every structure of UniProt Q5J8M3
Every structure of UniProt Q8N4V1
Every structure of UniProt Q9BV81
Every structure of UniProt Q9NPA0
Every structure of UniProt O43402
Every structure of UniProt Q5UCC4
Elsewhere: RCSB PDB 7ADO · PDBe 7ADO · UniProt Q8N766 · UniProt Q15006 · UniProt Q9P0I2 · UniProt Q5J8M3 · UniProt Q8N4V1 · UniProt Q9BV81 · UniProt Q9NPA0 · UniProt O43402 · UniProt Q5UCC4

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