SMTL ID : 6xs9.1 (1 other biounit)

Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-1-3-mer

Ligands

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 3 residues within 4Å: Chain A: M.106, F.132, H.134 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.132 Salt bridges: A:H.134 MLI.2: 5 residues within 4Å: Chain A: H.67, I.68, Y.79, P.80, K.83 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.80 Hydrogen bonds: A:I.68 Salt bridges: A:H.67, A:K.83

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Q.82, V.84, Q.115, F.116 Chain C: P.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.82 GOL.4: 7 residues within 4Å: Chain A: K.91, Q.113, D.117, V.118, D.119, K.137, K.191 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.117, A:V.118, A:K.137, A:K.191 GOL.5: 1 residues within 4Å: Chain D: K.4 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, K.E. et al., De novo macrocyclic peptides for inhibiting, stabilizing, and probing the function of the retromer endosomal trafficking complex. Sci Adv (2021)

Release Date

2021-07-21

Peptides

Vacuolar protein sorting-associated protein 29: A
48V-TYR-ILE-LYS-THR-PRO-LEU-GLY-THR-PHE-PRO-ASN-ARG-HIS-GLY: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
F

Vacuolar protein sorting-associated protein 29

48V-TYR-ILE-LYS-THR-PRO-LEU-GLY-THR-PHE-PRO-ASN-ARG-HIS-GLY

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