SMTL ID : 3nz1.1

Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

1 x 3NY: 5-nitro-1H-benzotriazole(Non-covalent)

3NY.1: 9 residues within 4Å: Chain A: A.51, K.53, A.81, A.83, W.110, E.178, W.210, Q.211 Ligands: SO4.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.81, A:W.110, A:W.210 Hydrogen bonds: A:E.178, A:Q.211 pi-Stacking: A:W.110, A:W.110, A:W.110, A:W.210

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

SO4.2: 3 residues within 4Å: Chain A: R.3, Y.4, T.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.4 Water bridges: A:R.3 SO4.3: 3 residues within 4Å: Chain A: R.36, F.40, R.43 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.36, A:R.43 SO4.4: 9 residues within 4Å: Chain A: K.53, R.182, W.210, Q.211, G.212, I.232, G.233, S.234 Ligands: SO4.6 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.182, A:G.212, A:G.233, A:S.234, A:S.234 Water bridges: A:K.53, A:K.53, A:K.53, A:S.56, A:S.58, A:Q.211, A:Q.211, A:Q.211, A:S.235 Salt bridges: A:K.53 SO4.5: 1 residues within 4Å: Chain A: K.10 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.10 SO4.6: 8 residues within 4Å: Chain A: K.53, S.56, S.58, F.89, R.182, Q.211 Ligands: 3NY.1, SO4.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.56, A:S.58, A:S.58, A:S.58, A:Q.211 Water bridges: A:R.182 Salt bridges: A:K.53, A:R.182 SO4.7: 4 residues within 4Å: Chain A: P.20, S.21, R.23, S.117 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.21, A:S.21, A:S.117 Salt bridges: A:R.23, A:K.115

3 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.8: 6 residues within 4Å: Chain A: R.36, F.40, I.45, R.75, Y.76, I.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.36, A:R.75 Salt bridges: A:R.43 TLA.9: 3 residues within 4Å: Chain A: Y.148, S.151, Y.152 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.148, A:S.151, A:S.151 Water bridges: A:S.151 TLA.10: 1 residues within 4Å: Chain A: N.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Privett, H.K. et al., Iterative approach to computational enzyme design. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2011-06-29

Peptides

Indole-3-glycerol phosphate synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Indole-3-glycerol phosphate synthase

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