SMTL ID : 4bm9.1

Structure of the autoinhibited Parkin catalytic domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-hexamer

Ligands

48 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.14, C.18, C.76, H.79 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.14, A:C.18, A:C.76, A:H.79 ZN.2: 5 residues within 4Å: Chain A: C.117, H.121, C.153, A.155, C.157 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.117, A:H.121, A:C.153, A:C.157 ZN.3: 4 residues within 4Å: Chain A: C.310, C.313, C.321, H.325 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.310, A:C.313, A:C.321, A:H.325 ZN.4: 5 residues within 4Å: Chain A: C.30, T.32, C.33, C.60, C.65 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.30, A:C.33, A:C.60, A:C.65 ZN.5: 4 residues within 4Å: Chain A: C.102, C.105, C.124, C.127 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.102, A:C.105, A:C.124, A:C.127 ZN.6: 4 residues within 4Å: Chain A: C.196, C.201, C.216, E.217 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.196, A:C.201, A:C.216 ZN.7: 4 residues within 4Å: Chain A: C.229, C.232, H.237, C.241 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.229, A:H.237, A:C.241 ZN.8: 4 residues within 4Å: Chain A: C.282, C.285, C.300, C.305 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.282, A:C.285, A:C.300, A:C.305 ZN.13: 4 residues within 4Å: Chain B: C.14, C.18, C.76, H.79 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.14, B:C.18, B:C.76, B:H.79 ZN.14: 5 residues within 4Å: Chain B: C.117, H.121, C.153, A.155, C.157 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.117, B:H.121, B:C.153, B:C.157 ZN.15: 4 residues within 4Å: Chain B: C.310, C.313, C.321, H.325 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.310, B:C.313, B:C.321, B:H.325 ZN.16: 5 residues within 4Å: Chain B: C.30, T.32, C.33, C.60, C.65 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.30, B:C.33, B:C.60, B:C.65 ZN.17: 4 residues within 4Å: Chain B: C.102, C.105, C.124, C.127 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.102, B:C.105, B:C.124, B:C.127 ZN.18: 4 residues within 4Å: Chain B: C.196, C.201, C.216, E.217 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.196, B:C.201, B:C.216 ZN.19: 4 residues within 4Å: Chain B: C.229, C.232, H.237, C.241 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.229, B:H.237, B:C.241 ZN.20: 4 residues within 4Å: Chain B: C.282, C.285, C.300, C.305 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.282, B:C.285, B:C.300, B:C.305 ZN.25: 4 residues within 4Å: Chain C: C.14, C.18, C.76, H.79 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.14, C:C.18, C:C.76, C:H.79 ZN.26: 5 residues within 4Å: Chain C: C.117, H.121, C.153, A.155, C.157 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.117, C:H.121, C:C.153, C:C.157 ZN.27: 4 residues within 4Å: Chain C: C.310, C.313, C.321, H.325 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.310, C:C.313, C:C.321, C:H.325 ZN.28: 5 residues within 4Å: Chain C: C.30, T.32, C.33, C.60, C.65 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.30, C:C.33, C:C.60, C:C.65 ZN.29: 4 residues within 4Å: Chain C: C.102, C.105, C.124, C.127 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.102, C:C.105, C:C.124, C:C.127 ZN.30: 4 residues within 4Å: Chain C: C.196, C.201, C.216, E.217 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.196, C:C.201, C:C.216 ZN.31: 4 residues within 4Å: Chain C: C.229, C.232, H.237, C.241 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.229, C:H.237, C:C.241 ZN.32: 4 residues within 4Å: Chain C: C.282, C.285, C.300, C.305 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.282, C:C.285, C:C.300, C:C.305 ZN.37: 4 residues within 4Å: Chain D: C.14, C.18, C.76, H.79 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.14, D:C.18, D:C.76, D:H.79 ZN.38: 5 residues within 4Å: Chain D: C.117, H.121, C.153, A.155, C.157 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.117, D:H.121, D:C.153, D:C.157 ZN.39: 4 residues within 4Å: Chain D: C.310, C.313, C.321, H.325 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.310, D:C.313, D:C.321, D:H.325 ZN.40: 5 residues within 4Å: Chain D: C.30, T.32, C.33, C.60, C.65 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.30, D:C.33, D:C.60, D:C.65 ZN.41: 4 residues within 4Å: Chain D: C.102, C.105, C.124, C.127 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.102, D:C.105, D:C.124, D:C.127 ZN.42: 4 residues within 4Å: Chain D: C.196, C.201, C.216, E.217 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.196, D:C.201, D:C.216 ZN.43: 4 residues within 4Å: Chain D: C.229, C.232, H.237, C.241 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.229, D:H.237, D:C.241 ZN.44: 4 residues within 4Å: Chain D: C.282, C.285, C.300, C.305 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.282, D:C.285, D:C.300, D:C.305 ZN.49: 4 residues within 4Å: Chain E: C.14, C.18, C.76, H.79 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.14, E:C.18, E:C.76, E:H.79 ZN.50: 5 residues within 4Å: Chain E: C.117, H.121, C.153, A.155, C.157 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.117, E:H.121, E:C.153, E:C.157 ZN.51: 4 residues within 4Å: Chain E: C.310, C.313, C.321, H.325 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.310, E:C.313, E:C.321, E:H.325 ZN.52: 5 residues within 4Å: Chain E: C.30, T.32, C.33, C.60, C.65 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.30, E:C.33, E:C.60, E:C.65 ZN.53: 4 residues within 4Å: Chain E: C.102, C.105, C.124, C.127 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.102, E:C.105, E:C.124, E:C.127 ZN.54: 4 residues within 4Å: Chain E: C.196, C.201, C.216, E.217 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.196, E:C.201, E:C.216 ZN.55: 4 residues within 4Å: Chain E: C.229, C.232, H.237, C.241 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.229, E:H.237, E:C.241 ZN.56: 4 residues within 4Å: Chain E: C.282, C.285, C.300, C.305 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.282, E:C.285, E:C.300, E:C.305 ZN.61: 4 residues within 4Å: Chain F: C.14, C.18, C.76, H.79 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.14, F:C.18, F:C.76, F:H.79 ZN.62: 5 residues within 4Å: Chain F: C.117, H.121, C.153, A.155, C.157 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.117, F:H.121, F:C.153, F:C.157 ZN.63: 4 residues within 4Å: Chain F: C.310, C.313, C.321, H.325 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.310, F:C.313, F:C.321, F:H.325 ZN.64: 5 residues within 4Å: Chain F: C.30, T.32, C.33, C.60, C.65 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.30, F:C.33, F:C.60, F:C.65 ZN.65: 4 residues within 4Å: Chain F: C.102, C.105, C.124, C.127 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.102, F:C.105, F:C.124, F:C.127 ZN.66: 4 residues within 4Å: Chain F: C.196, C.201, C.216, E.217 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.196, F:C.201, F:C.216 ZN.67: 4 residues within 4Å: Chain F: C.229, C.232, H.237, C.241 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.229, F:H.237, F:C.241 ZN.68: 4 residues within 4Å: Chain F: C.282, C.285, C.300, C.305 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.282, F:C.285, F:C.300, F:C.305

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

SO4.9: 4 residues within 4Å: Chain A: R.27, K.75, T.81 Chain D: R.284 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: N.318, R.319 Chain D: N.318, R.319 Ligands: SO4.46 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: K.15, H.166, R.169, Y.176 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain B: R.27, K.75, T.81 Chain C: R.284 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain B: N.318, R.319 Chain C: N.318, R.319 Ligands: SO4.34 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain B: K.15, H.166, R.169, Y.176 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain B: R.284 Chain C: R.27, K.75, T.81 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain B: N.318, R.319 Chain C: N.318, R.319 Ligands: SO4.22 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain C: K.15, H.166, R.169, Y.176 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain A: R.284 Chain D: R.27, K.75, T.81 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain A: N.318, R.319 Chain D: N.318, R.319 Ligands: SO4.10 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain D: K.15, H.166, R.169, Y.176 Ligand excluded by PLIP SO4.57: 4 residues within 4Å: Chain E: R.27, K.75, T.81 Chain F: R.284 Ligand excluded by PLIP SO4.58: 5 residues within 4Å: Chain E: N.318, R.319 Chain F: N.318, R.319 Ligands: SO4.70 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain E: K.15, H.166, R.169, Y.176 Ligand excluded by PLIP SO4.69: 4 residues within 4Å: Chain E: R.284 Chain F: R.27, K.75, T.81 Ligand excluded by PLIP SO4.70: 5 residues within 4Å: Chain E: N.318, R.319 Chain F: N.318, R.319 Ligands: SO4.58 Ligand excluded by PLIP SO4.71: 4 residues within 4Å: Chain F: K.15, H.166, R.169, Y.176 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 3 residues within 4Å: Chain A: K.280, W.311, N.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.280, A:N.312 GOL.24: 3 residues within 4Å: Chain B: K.280, W.311, N.312 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.280, B:N.312 GOL.36: 3 residues within 4Å: Chain C: K.280, W.311, N.312 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.280, C:N.312 GOL.48: 3 residues within 4Å: Chain D: K.280, W.311, N.312 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.280, D:N.312 GOL.60: 3 residues within 4Å: Chain E: K.280, W.311, N.312 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.280, E:N.312 GOL.72: 3 residues within 4Å: Chain F: K.280, W.311, N.312 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.280, F:N.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wauer, T. et al., Structure of the Human Parkin Ligase Domain in an Autoinhibited State. Embo J. (2013)

Release Date

2013-06-12

Peptides

E3 UBIQUITIN-PROTEIN LIGASE PARKIN: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

E3 UBIQUITIN-PROTEIN LIGASE PARKIN