SMTL ID : 7ynx.1 (1 other biounit)

Crystal structure of Pirh2 bound to poly-Ala peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: A.32, C.34, C.35, H.45, H.51 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.34, A:C.35, A:H.45, A:H.51 ZN.2: 4 residues within 4Å: Chain A: C.63, C.66, C.76, C.79 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.63, A:C.66, A:C.76, A:C.79 ZN.3: 5 residues within 4Å: Chain A: C.103, C.106, H.119, L.125, C.126 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.103, A:C.106, A:H.119, A:C.126 ZN.4: 4 residues within 4Å: Chain A: C.165, H.167, C.184, C.187 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.165, A:H.167, A:C.184, A:C.187 ZN.5: 4 residues within 4Å: Chain A: C.21, H.23, C.41, C.44 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.21, A:H.23, A:C.41, A:C.44 ZN.6: 5 residues within 4Å: Chain A: C.88, C.91, H.102, I.108, C.109 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.88, A:C.91, A:H.102, A:C.109 ZN.7: 4 residues within 4Å: Chain A: C.146, C.149, H.170, C.173 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.146, A:C.149, A:H.170, A:C.173 ZN.8: 4 residues within 4Å: Chain A: C.120, C.123, H.135, C.137 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.120, A:C.123, A:H.135, A:C.137

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 1 residues within 4Å: Chain A: R.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.16, A:R.16 SO4.10: 2 residues within 4Å: Chain A: K.96, K.98 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.96, A:K.98

7 x NA: SODIUM ION(Non-functional Binders)

NA.11: 2 residues within 4Å: Chain A: R.19, G.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.20, A:G.20 NA.12: 4 residues within 4Å: Chain A: R.26, L.30, C.41, R.42 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.26, A:R.26, A:R.42, A:R.42 Water bridges: A:H.92 NA.13: 1 residues within 4Å: Chain A: C.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.106 NA.14: 2 residues within 4Å: Chain A: K.114, H.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.114, A:K.114, A:H.119 NA.15: 1 residues within 4Å: Chain A: V.159 No protein-ligand interaction detected (PLIP) NA.16: 1 residues within 4Å: Chain A: N.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.124 NA.17: 1 residues within 4Å: Chain A: H.170 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., Recognition of an Ala-rich C-degron by the E3 ligase Pirh2. Nat Commun (2023)

Release Date

2023-04-26

Peptides

RING finger and CHY zinc finger domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RING finger and CHY zinc finger domain-containing protein 1

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