SMTL ID : 3wwp.1 (2 other biounits)

S-selective hydroxynitrile lyase from Baliospermum montanum (apo2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 7 residues within 4Å: Chain A: P.187, S.265, K.266, V.267, N.268, E.269 Ligands: SO4.8 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.267, A:N.268 Water bridges: A:S.265, A:K.266, A:K.266, A:K.266, A:N.268, A:N.268, A:N.268 Salt bridges: A:K.46, A:K.266, A:K.266 CIT.10: 6 residues within 4Å: Chain B: P.187, S.265, K.266, V.267, N.268, E.269 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:V.267, B:N.268, B:N.268 Water bridges: B:S.265, B:K.266, B:E.269 Salt bridges: B:K.46, B:K.266, B:K.266

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: T.36, I.37, S.105, I.234 Ligands: CL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.36, A:S.105 EDO.3: 3 residues within 4Å: Chain A: V.149, D.238, F.239 No protein-ligand interaction detected (PLIP) EDO.4: 2 residues within 4Å: Chain A: Y.161, T.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.162 Water bridges: A:T.162 EDO.5: 5 residues within 4Å: Chain A: Y.143, W.153, F.158, T.169, F.203 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.143 EDO.11: 5 residues within 4Å: Chain B: T.36, I.37, S.105, F.203 Ligands: CL.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.36, B:I.37 Water bridges: B:S.105 EDO.12: 11 residues within 4Å: Chain A: I.68, D.69, P.70, Q.72, R.199 Chain B: I.68, D.69, P.70, R.71, Q.72, R.199 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.199, B:Q.72, B:R.199 EDO.13: 6 residues within 4Å: Chain B: L.113, E.116, P.139, L.211, P.212, F.214 No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain B: Y.143, W.153, F.158, V.171, F.203 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.143 Water bridges: B:Y.143

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

SO4.6: 3 residues within 4Å: Chain A: H.137, S.138, F.141 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.138 Water bridges: A:D.136, A:S.138, A:N.213 Salt bridges: A:K.144 SO4.7: 2 residues within 4Å: Chain A: K.154, R.176 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.154, A:K.154, A:K.154, A:R.176 Salt bridges: A:R.176 SO4.8: 4 residues within 4Å: Chain A: N.185, S.257, K.266 Ligands: CIT.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.185, A:S.257 Water bridges: A:K.266, A:K.266, A:K.266, A:K.266 Salt bridges: A:K.266 SO4.15: 3 residues within 4Å: Chain B: H.137, S.138, F.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.138 Water bridges: B:K.144 Salt bridges: B:H.137, B:K.144 SO4.16: 2 residues within 4Å: Chain B: K.154, R.176 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.154, B:K.154, B:K.154, B:K.154 Salt bridges: B:R.176 SO4.17: 1 residues within 4Å: Chain B: K.251 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.223, B:Y.253 Salt bridges: B:K.251 SO4.18: 4 residues within 4Å: Chain B: S.28, A.29, H.30, K.97 6 PLIP interactions: 6 interactions with chain B Water bridges: B:H.30, B:H.30, B:K.98, B:K.98, B:K.98 Salt bridges: B:K.97 SO4.19: 3 residues within 4Å: Chain B: F.141, K.145, W.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.242 Salt bridges: B:K.145

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

CL.9: 7 residues within 4Å: Chain A: T.36, H.39, S.105, I.182, H.260, K.261 Ligands: EDO.2 Ligand excluded by PLIP CL.20: 7 residues within 4Å: Chain B: T.36, H.39, S.105, I.182, H.260, K.261 Ligands: EDO.11 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakano, S. et al., Structural and functional analysis of hydroxynitrile lyase from Baliospermum montanum with crystal structure, molecular dynamics and enzyme kinetics. Biochim.Biophys.Acta (2014)

Release Date

2014-10-22

Peptides

(S)-hydroxynitrile lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

(S)-hydroxynitrile lyase

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