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Structural analysis of the ternary complex between lamin A/C, baf and emerin identifies an interface disrupted in autosomal recessive progeroid diseases

Analyse Structural analysis of the ternary complex between lamin A/C, baf and emerin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GHD
Type: protein
Length: 675 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Emerin; Barrier-to-autointegration factor; Prelamin-A/C
UniProt: P50402, O75531, P02545
Ligands: SO4
Pockets: 9 · best druggability 0.39

Structure

x-ray diffraction · 6 distinct chains · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Emerin	protein	45	58% helix, 0% strand	P50402
D, C	Barrier-to-autointegration factor	protein	87	68% helix, 2% strand	O75531
B	Prelamin-A/C	protein	119	3% helix, 50% strand	P02545
E, A	Barrier-to-autointegration factor	protein	88	67% helix, 2% strand	O75531
F	Prelamin-A/C	protein	118	3% helix, 51% strand	P02545
H	Emerin	protein	43	53% helix, 0% strand	P50402

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains G, D, E, A, C, H
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	141	0.39	0.73	24	empty
2	111	0.36	0.73	20	empty
3	84	0.32	0.74	15	empty
4	52	0.29	0.76	15	empty
5	65	0.29	0.74	18	empty

Interfaces

14 interfaces between chains.

D–E · 757 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 755 Å² buried · 10 hydrogen bonds · protein-protein
G–D · 406 Å² buried · 5 hydrogen bonds · protein-protein
C–H · 405 Å² buried · 6 hydrogen bonds · protein-protein
D–B · 297 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6GHD · Structural analysis of the ternary complex between lamin A/C, BAF and emerin identifies… · the same entry in another collection · chain H against H, TM-score 1.00
P02545 · AlphaFold monomer V2.0 prediction for prelamin-A/C (P02545) · a predicted model of the same protein · chain F against A, TM-score 0.99
O75531 · AlphaFold monomer V2.0 prediction for barrier-to-autointegration factor (O75531) · a predicted model of the same protein · chain D 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 P50402
Every structure of UniProt O75531
Every structure of UniProt P02545
Elsewhere: RCSB PDB 6GHD · PDBe 6GHD · UniProt P50402 · UniProt O75531 · UniProt P02545

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