SMTL ID : 3u13.1

Crystal Structure of de Novo design of cystein esterase ECH13 at the resolution 1.6A, Northeast Structural Genomics Consortium Target OR51

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 10 residues within 4Å: Chain A: D.11, M.12, D.13, Y.45, T.100, S.101, H.103, K.113, K.135 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.13, A:D.13, A:D.13, A:Y.45, A:S.101 Water bridges: A:S.101, A:K.135, A:K.135, A:K.135 Salt bridges: A:H.103, A:K.113, A:K.135 PO4.3: 6 residues within 4Å: Chain A: E.67, M.105, K.107, Y.108 Ligands: NA.5, PEG.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.67, A:K.107 PO4.6: 10 residues within 4Å: Chain B: D.11, M.12, D.13, Y.45, T.100, S.101, H.103, K.113, K.135 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.13, B:D.13, B:T.100, B:S.101 Water bridges: B:S.101, B:K.135, B:K.135, B:K.135 Salt bridges: B:H.103, B:K.113, B:K.135 PO4.8: 6 residues within 4Å: Chain B: E.67, M.105, K.107, Y.108 Ligands: PEG.4, NA.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.67, B:K.107

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.11, D.13, Y.45, D.145, D.146 Ligands: PO4.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.11, A:D.13, A:D.146, H2O.3, H2O.7 MG.7: 6 residues within 4Å: Chain B: D.11, D.13, Y.45, D.145, D.146 Ligands: PO4.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.11, B:D.13, B:D.146, H2O.12, H2O.16

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 7 residues within 4Å: Chain A: E.118, P.123, L.126 Chain B: K.104, M.105, F.106 Ligands: PO4.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.106 PEG.9: 7 residues within 4Å: Chain A: K.104, M.105, F.106 Chain B: E.118, P.123, L.126 Ligands: PO4.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.118, A:F.106

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

NA.5: 6 residues within 4Å: Chain A: M.105, F.106, K.107, Y.108, C.109 Ligands: PO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.107, A:Y.108, A:C.109 Water bridges: A:E.67 NA.10: 6 residues within 4Å: Chain B: M.105, F.106, K.107, Y.108, C.109 Ligands: PO4.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.107, B:Y.108, B:C.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Richter, F. et al., Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. J.Am.Chem.Soc. (2012)

Release Date

2011-11-23

Peptides

artificial protein OR51: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

artificial protein OR51

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