MolNFT v1 · #162999 · protein

Lem domain of emerin mutant T43I in complex with baf dimer and the igfold of the lamin A/C

6RPR · Prelamin-A/C: “Lem domain of emerin mutant T43I in complex with baf dimer and the igfold of the lamin A/C”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.37). MolNFT v1 #162999 on GenesisL1: 3D structure, binding…

PDB: 6RPR
Type: protein
Length: 333 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prelamin-A/C; Barrier to autointegration factor (baf); Lem domain of emerin mutant T43I
UniProt: P02545
Ligands: SO4
Pockets: 2 · best druggability 0.37

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Prelamin-A/C	protein	116	3% helix, 50% strand	P02545
D, E	Barrier to autointegration factor (baf)	protein	87	68% helix, 2% strand	—
G	Lem domain of emerin mutant T43I	protein	43	51% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains D

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

Pockets

2 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	118	0.37	0.74	21	empty
2	64	0.33	0.76	13	empty

Interfaces

5 interfaces between chains.

D–E · 761 Å² buried · 8 hydrogen bonds · protein-protein
D–G · 438 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 301 Å² buried · 6 hydrogen bonds · protein-protein
E–G · 300 Å² buried · 2 hydrogen bonds · protein-protein
B–E · 215 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6RPR · LEM domain of Emerin mutant T43I in complex with BAF dimer and the Igfold of the lamin A/C · the same entry in another collection · chain B against B, TM-score 1.00
P02545 · AlphaFold monomer V2.0 prediction for prelamin-A/C (P02545) · 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 P02545
Elsewhere: RCSB PDB 6RPR · PDBe 6RPR · UniProt P02545

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