SMTL ID : 2wzn.1

3d structure of TET3 from Pyrococcus horikoshii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-12-mer

Ligands

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: Y.27, F.109, T.163, V.164 Ligand excluded by PLIP GOL.2: 4 residues within 4Å: Chain A: R.173, L.174, N.175, E.176 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain B: Y.27, F.109, T.163, V.164 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain B: R.173, L.174, N.175, E.176 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain C: Y.27, F.109, T.163, V.164 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain C: R.173, L.174, N.175, E.176 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain D: Y.27, F.109, T.163, V.164 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain D: R.173, L.174, N.175, E.176 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain E: Y.27, F.109, T.163, V.164 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain E: R.173, L.174, N.175, E.176 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain F: Y.27, F.109, T.163, V.164 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain F: R.173, L.174, N.175, E.176 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain G: Y.27, F.109, T.163, V.164 Ligand excluded by PLIP GOL.38: 4 residues within 4Å: Chain G: R.173, L.174, N.175, E.176 Ligand excluded by PLIP GOL.43: 4 residues within 4Å: Chain H: Y.27, F.109, T.163, V.164 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain H: R.173, L.174, N.175, E.176 Ligand excluded by PLIP GOL.49: 4 residues within 4Å: Chain I: Y.27, F.109, T.163, V.164 Ligand excluded by PLIP GOL.50: 4 residues within 4Å: Chain I: R.173, L.174, N.175, E.176 Ligand excluded by PLIP GOL.55: 4 residues within 4Å: Chain J: Y.27, F.109, T.163, V.164 Ligand excluded by PLIP GOL.56: 4 residues within 4Å: Chain J: R.173, L.174, N.175, E.176 Ligand excluded by PLIP GOL.61: 4 residues within 4Å: Chain K: Y.27, F.109, T.163, V.164 Ligand excluded by PLIP GOL.62: 4 residues within 4Å: Chain K: R.173, L.174, N.175, E.176 Ligand excluded by PLIP GOL.67: 4 residues within 4Å: Chain L: Y.27, F.109, T.163, V.164 Ligand excluded by PLIP GOL.68: 4 residues within 4Å: Chain L: R.173, L.174, N.175, E.176 Ligand excluded by PLIP

24 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: D.185, E.216, H.322 Ligands: ZN.4, CL.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.185, A:E.216, A:E.216, A:H.322, H2O.9 ZN.4: 8 residues within 4Å: Chain A: H.71, D.185, D.186, E.215, E.216, D.238 Ligands: ZN.3, CL.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.71, A:D.185, A:D.238, A:D.238 ZN.9: 5 residues within 4Å: Chain B: D.185, E.216, H.322 Ligands: ZN.10, CL.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.185, B:E.216, B:E.216, B:H.322, H2O.17 ZN.10: 8 residues within 4Å: Chain B: H.71, D.185, D.186, E.215, E.216, D.238 Ligands: ZN.9, CL.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.71, B:D.185, B:D.238, B:D.238 ZN.15: 5 residues within 4Å: Chain C: D.185, E.216, H.322 Ligands: ZN.16, CL.17 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.185, C:E.216, C:E.216, C:H.322, H2O.25 ZN.16: 8 residues within 4Å: Chain C: H.71, D.185, D.186, E.215, E.216, D.238 Ligands: ZN.15, CL.17 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.71, C:D.185, C:D.238, C:D.238 ZN.21: 5 residues within 4Å: Chain D: D.185, E.216, H.322 Ligands: ZN.22, CL.23 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.185, D:E.216, D:E.216, D:H.322, H2O.34 ZN.22: 8 residues within 4Å: Chain D: H.71, D.185, D.186, E.215, E.216, D.238 Ligands: ZN.21, CL.23 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.71, D:D.185, D:D.238, D:D.238 ZN.27: 5 residues within 4Å: Chain E: D.185, E.216, H.322 Ligands: ZN.28, CL.29 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.185, E:E.216, E:E.216, E:H.322, H2O.42 ZN.28: 8 residues within 4Å: Chain E: H.71, D.185, D.186, E.215, E.216, D.238 Ligands: ZN.27, CL.29 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.71, E:D.185, E:D.238, E:D.238 ZN.33: 5 residues within 4Å: Chain F: D.185, E.216, H.322 Ligands: ZN.34, CL.35 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.185, F:E.216, F:E.216, F:H.322, H2O.50 ZN.34: 8 residues within 4Å: Chain F: H.71, D.185, D.186, E.215, E.216, D.238 Ligands: ZN.33, CL.35 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.71, F:D.185, F:D.238, F:D.238 ZN.39: 5 residues within 4Å: Chain G: D.185, E.216, H.322 Ligands: ZN.40, CL.41 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.185, G:E.216, G:E.216, G:H.322, H2O.59 ZN.40: 8 residues within 4Å: Chain G: H.71, D.185, D.186, E.215, E.216, D.238 Ligands: ZN.39, CL.41 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.71, G:D.185, G:D.238, G:D.238 ZN.45: 5 residues within 4Å: Chain H: D.185, E.216, H.322 Ligands: ZN.46, CL.47 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.185, H:E.216, H:E.216, H:H.322, H2O.67 ZN.46: 8 residues within 4Å: Chain H: H.71, D.185, D.186, E.215, E.216, D.238 Ligands: ZN.45, CL.47 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.71, H:D.185, H:D.238, H:D.238 ZN.51: 5 residues within 4Å: Chain I: D.185, E.216, H.322 Ligands: ZN.52, CL.53 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.185, I:E.216, I:E.216, I:H.322, H2O.75 ZN.52: 8 residues within 4Å: Chain I: H.71, D.185, D.186, E.215, E.216, D.238 Ligands: ZN.51, CL.53 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.71, I:D.185, I:D.238, I:D.238 ZN.57: 5 residues within 4Å: Chain J: D.185, E.216, H.322 Ligands: ZN.58, CL.59 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.185, J:E.216, J:E.216, J:H.322, H2O.84 ZN.58: 8 residues within 4Å: Chain J: H.71, D.185, D.186, E.215, E.216, D.238 Ligands: ZN.57, CL.59 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.71, J:D.185, J:D.238, J:D.238 ZN.63: 5 residues within 4Å: Chain K: D.185, E.216, H.322 Ligands: ZN.64, CL.65 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.185, K:E.216, K:E.216, K:H.322, H2O.92 ZN.64: 8 residues within 4Å: Chain K: H.71, D.185, D.186, E.215, E.216, D.238 Ligands: ZN.63, CL.65 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.71, K:D.185, K:D.238, K:D.238 ZN.69: 5 residues within 4Å: Chain L: D.185, E.216, H.322 Ligands: ZN.70, CL.71 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:D.185, L:E.216, L:E.216, L:H.322, H2O.100 ZN.70: 8 residues within 4Å: Chain L: H.71, D.185, D.186, E.215, E.216, D.238 Ligands: ZN.69, CL.71 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:H.71, L:D.185, L:D.238, L:D.238

24 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 7 residues within 4Å: Chain A: H.71, D.185, E.215, E.216, D.238 Ligands: ZN.3, ZN.4 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: R.65, N.230 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain B: H.71, D.185, E.215, E.216, D.238 Ligands: ZN.9, ZN.10 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: R.65, N.230 Ligand excluded by PLIP CL.17: 7 residues within 4Å: Chain C: H.71, D.185, E.215, E.216, D.238 Ligands: ZN.15, ZN.16 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: R.65, N.230 Ligand excluded by PLIP CL.23: 7 residues within 4Å: Chain D: H.71, D.185, E.215, E.216, D.238 Ligands: ZN.21, ZN.22 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain D: R.65, N.230 Ligand excluded by PLIP CL.29: 7 residues within 4Å: Chain E: H.71, D.185, E.215, E.216, D.238 Ligands: ZN.27, ZN.28 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain E: R.65, N.230 Ligand excluded by PLIP CL.35: 7 residues within 4Å: Chain F: H.71, D.185, E.215, E.216, D.238 Ligands: ZN.33, ZN.34 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain F: R.65, N.230 Ligand excluded by PLIP CL.41: 7 residues within 4Å: Chain G: H.71, D.185, E.215, E.216, D.238 Ligands: ZN.39, ZN.40 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain G: R.65, N.230 Ligand excluded by PLIP CL.47: 7 residues within 4Å: Chain H: H.71, D.185, E.215, E.216, D.238 Ligands: ZN.45, ZN.46 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain H: R.65, N.230 Ligand excluded by PLIP CL.53: 7 residues within 4Å: Chain I: H.71, D.185, E.215, E.216, D.238 Ligands: ZN.51, ZN.52 Ligand excluded by PLIP CL.54: 2 residues within 4Å: Chain I: R.65, N.230 Ligand excluded by PLIP CL.59: 7 residues within 4Å: Chain J: H.71, D.185, E.215, E.216, D.238 Ligands: ZN.57, ZN.58 Ligand excluded by PLIP CL.60: 2 residues within 4Å: Chain J: R.65, N.230 Ligand excluded by PLIP CL.65: 7 residues within 4Å: Chain K: H.71, D.185, E.215, E.216, D.238 Ligands: ZN.63, ZN.64 Ligand excluded by PLIP CL.66: 2 residues within 4Å: Chain K: R.65, N.230 Ligand excluded by PLIP CL.71: 7 residues within 4Å: Chain L: H.71, D.185, E.215, E.216, D.238 Ligands: ZN.69, ZN.70 Ligand excluded by PLIP CL.72: 2 residues within 4Å: Chain L: R.65, N.230 Ligand excluded by PLIP

Links

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Citation

Dura, M.A. et al., The Structural and Biochemical Characterizations of a Novel Tet Peptidase Complex from Pyrococcus Horikoshii Reveal an Integrated Peptide Degradation System in Hyperthermophilic Archaea. Mol.Microbiol. (2009)

Release Date

2010-11-03

Peptides

354AA LONG HYPOTHETICAL OPERON PROTEIN FRV: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

354AA LONG HYPOTHETICAL OPERON PROTEIN FRV