SMTL ID : 4keq.2 (1 other biounit)

Crystal structure of 4-pyridoxolactonase, 5-pyridoxolactone bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.100, H.101, D.207, H.252 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.100, A:H.101, A:D.207, A:H.252, H2O.1 ZN.2: 5 residues within 4Å: Chain A: H.96, H.98, H.185, D.207 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.96, A:H.98, A:H.185, A:D.207, H2O.1 ZN.11: 5 residues within 4Å: Chain B: D.100, H.101, D.207, H.252 Ligands: ZN.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.100, B:H.101, B:D.207, B:H.252, H2O.2 ZN.12: 5 residues within 4Å: Chain B: H.96, H.98, H.185, D.207 Ligands: ZN.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.96, B:H.98, B:H.185, B:D.207, H2O.2

4 x 5PN: 7-hydroxy-6-methylfuro[3,4-c]pyridin-3(1H)-one(Non-covalent)

5PN.3: 10 residues within 4Å: Chain A: L.16, F.33, E.65, H.98, F.99, D.100, L.132, G.133, Y.210, F.223 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.16, A:F.33, A:F.99 Hydrogen bonds: A:D.100 Salt bridges: A:H.98 pi-Stacking: A:H.98, A:F.99, A:F.223, A:F.223 5PN.4: 9 residues within 4Å: Chain A: D.10, G.12, S.13, I.68, E.70, Q.73, M.254, F.257, K.258 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.68 Hydrogen bonds: A:E.70, A:Q.73 Salt bridges: A:K.258 5PN.13: 10 residues within 4Å: Chain B: L.16, F.33, E.65, H.98, F.99, D.100, L.132, G.133, Y.210, F.223 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.16, B:F.33, B:F.99 Hydrogen bonds: B:D.100, B:Y.210 Salt bridges: B:H.98 pi-Stacking: B:H.98, B:F.99, B:F.223, B:F.223 5PN.14: 9 residues within 4Å: Chain B: D.10, G.12, S.13, I.68, E.70, Q.73, M.254, F.257, K.258 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.68 Hydrogen bonds: B:E.70, B:Q.73 Salt bridges: B:K.258

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: C.115, H.116, R.117, V.120, P.121, F.164, G.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.116, A:V.120 Water bridges: A:E.142, A:F.164 GOL.6: 2 residues within 4Å: Chain A: E.142, R.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.142, A:R.159, A:R.159 GOL.7: 8 residues within 4Å: Chain A: F.22, V.31, R.32, F.33, T.211, H.252, D.253, M.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.32, A:H.252, A:M.254 GOL.15: 7 residues within 4Å: Chain B: C.115, H.116, R.117, V.120, P.121, F.164, G.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.116, B:V.120 Water bridges: B:E.142, B:F.164 GOL.16: 2 residues within 4Å: Chain B: E.142, R.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.159, B:R.159 GOL.17: 8 residues within 4Å: Chain B: F.22, V.31, R.32, F.33, T.211, H.252, D.253, M.254 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.32, B:H.252, B:D.253, B:M.254

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

EDO.8: 6 residues within 4Å: Chain A: D.54, H.57, K.106, D.136, S.138, Q.152 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.106, A:D.136, A:S.138 EDO.9: 2 residues within 4Å: Chain A: R.32, M.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.32 EDO.10: 4 residues within 4Å: Chain A: N.125, P.126, Q.127, P.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.125 Water bridges: A:Q.122 EDO.18: 6 residues within 4Å: Chain B: D.54, H.57, K.106, D.136, S.138, Q.152 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.106, B:D.136, B:S.138 EDO.19: 2 residues within 4Å: Chain B: R.32, M.254 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.32 EDO.20: 4 residues within 4Å: Chain B: N.125, P.126, Q.127, P.128 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.125 Water bridges: B:Q.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobayashi, J. et al., Structure of 4-pyridoxolactonase from Mesorhizobium loti. Acta Crystallogr.,Sect.F (2014)

Release Date

2014-04-09

Peptides

4-pyridoxolactonase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-pyridoxolactonase

Related Entries With Identical Sequence