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Crystal structure of chaetomium thermophilum VPS29 complexed with rapid-derived cyclic peptide rt-D3

Analyse Crystal structure of chaetomium thermophilum VPS29 complexed with rapid-derived… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XS8
Type: protein
Length: 196 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein 29…
UniProt: G0RZB5
Ligands: 48V

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolar protein sorting-associated protein 29	protein	184	14% helix, 40% strand	G0RZB5
B	48V-dty-gly-tyr-asp-pro-leu-gly-leu-lys-tyr-phe-ala	protein	12	0% helix, 17% strand	—

Ligands and binding sites

48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · chains B

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

Interfaces

1 interface between chains.

A–B · 420 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6XS8 · Crystal structure of Chaetomium thermophilum Vps29 complexed with RaPID-derived cyclic… · 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 G0RZB5
Elsewhere: RCSB PDB 6XS8 · PDBe 6XS8 · UniProt G0RZB5

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