MolNFT v1 · #169629 · protein

PCSK9(DELTACRD) in complex with cyclic peptide 40

6XIC · Proprotein convertase SUBTILISIN/KEXIN type 9: “PCSK9(DELTACRD) in complex with cyclic peptide 40”. X-ray diffraction, 2 ligands (B74, DHL). MolNFT v1 #169629 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XIC
Type: protein
Length: 390 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proprotein convertase SUBTILISIN/KEXIN type 9; Peptide 40
EC: 3.4.21.-
UniProt: Q8NBP7
Ligands: B74, DHL

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-)	protein	92	30% helix, 39% strand	Q8NBP7
B	Proprotein convertase SUBTILISIN/KEXIN type 9 (EC 3.4.21.-)	protein	289	30% helix, 24% strand	Q8NBP7
I	Peptide 40	protein	9	0% helix, 22% strand	—

Ligands and binding sites

B74 · (3-methylphenyl)methanol · ligand · chains B, I
DHL · 2-amino-ethanethiol · ligand · chains B, I
GOL · Glycerol · additive · chains A

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

Interfaces

2 interfaces between chains.

A–B · 1385 Å² buried · 29 hydrogen bonds · protein-protein
B–I · 510 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 3 modified, 2 covalent, 1 d-amino (disulfide, nonstandard, covalent ligand, D-amino acid).

Compared structures

6XIC · PCSK9(deltaCRD) in complex with cyclic peptide 40 · the same entry in another collection · chain A against A, 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 Q8NBP7
Elsewhere: RCSB PDB 6XIC · PDBe 6XIC · UniProt Q8NBP7

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