SMTL ID : 3c6z.1

HNL from Hevea brasiliensis to atomic resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.23 Chain B: F.150, E.167, K.170 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Water bridges: A:K.23, A:V.33, B:K.170, B:K.170, B:K.170 Salt bridges: A:K.23, B:K.170 SO4.2: 4 residues within 4Å: Chain A: T.137, K.138, D.139, G.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.139, A:G.140 Water bridges: A:K.138 SO4.3: 5 residues within 4Å: Chain A: T.110, K.191, G.195, K.199, Y.222 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.110, A:G.195, A:Y.222 Water bridges: A:K.191, A:K.199 Salt bridges: A:K.191 SO4.4: 3 residues within 4Å: Chain A: K.141, N.181, K.185 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.181 Water bridges: A:K.141, A:N.181, A:K.185 Salt bridges: A:K.141, A:K.185 SO4.8: 4 residues within 4Å: Chain A: F.150, E.167, K.170 Chain B: K.23 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Water bridges: B:K.23, B:V.33, A:K.170, A:K.170, A:K.170 Salt bridges: B:K.23, A:K.170 SO4.9: 4 residues within 4Å: Chain B: T.137, K.138, D.139, G.140 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.139, B:D.139, B:G.140 Water bridges: B:K.138 SO4.10: 5 residues within 4Å: Chain B: T.110, K.191, G.195, K.199, Y.222 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.110, B:G.195, B:Y.222 Water bridges: B:K.191, B:K.199 Salt bridges: B:K.191 SO4.11: 3 residues within 4Å: Chain B: K.141, N.181, K.185 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.181 Water bridges: B:K.141, B:N.181, B:K.185 Salt bridges: B:K.141, B:K.185

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.5: 4 residues within 4Å: Chain A: C.94, E.95, E.192, S.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.192 BME.12: 4 residues within 4Å: Chain B: C.94, E.95, E.192, S.196 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.192

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.6: 9 residues within 4Å: Chain A: T.11, I.12, S.80, C.81, W.128, L.148, L.157, I.209, F.210 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.12, A:L.148, A:I.209 Hydrogen bonds: A:T.11, A:S.80 IPA.13: 9 residues within 4Å: Chain B: T.11, I.12, S.80, C.81, W.128, L.148, L.157, I.209, F.210 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.12, B:L.148, B:I.209 Hydrogen bonds: B:T.11, B:S.80

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

PEG.7: 4 residues within 4Å: Chain A: Q.47, K.147, R.174, K.175 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.47, A:R.174, A:R.174, A:K.175 Water bridges: A:K.175, A:K.175 PEG.14: 4 residues within 4Å: Chain B: Q.47, K.147, R.174, K.175 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.47, B:R.174, B:R.174, B:K.175 Water bridges: B:K.175, B:K.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, A. et al., Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis. J.Biol.Chem. (2008)

Release Date

2008-06-03

Peptides

Hydroxynitrilase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hydroxynitrilase

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