SMTL ID : 3rwb.1

Crystal structure of complex of 4PAL (4-Pyridoxolactone) and PLDH (tetrameric pyridoxal 4-dehydrogenase) from Mesorhizobium loti

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 28 residues within 4Å: Chain A: G.13, A.15, Q.16, G.17, I.18, D.37, I.38, A.59, D.60, I.61, N.87, A.88, S.89, V.91, V.110, I.138, A.139, S.140, Y.153, K.157, P.183, G.184, L.185, I.186, S.188, G.190, V.191 Ligands: 4PL.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.183 Hydrogen bonds: A:Q.16, A:Q.16, A:I.18, A:I.38, A:D.60, A:D.60, A:I.61, A:N.87, A:Y.153, A:K.157, A:I.186, A:I.186, A:S.188, A:S.188, A:G.190 Water bridges: A:G.13, A:G.19, A:G.19 NAD.6: 28 residues within 4Å: Chain B: G.13, A.15, Q.16, G.17, I.18, D.37, I.38, A.59, D.60, I.61, N.87, A.88, S.89, V.91, V.110, I.138, A.139, S.140, Y.153, K.157, P.183, G.184, L.185, I.186, S.188, G.190, V.191 Ligands: 4PL.7 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:P.183 Hydrogen bonds: B:Q.16, B:I.18, B:I.38, B:D.60, B:I.61, B:N.87, B:K.157, B:I.186, B:I.186, B:S.188, B:S.188, B:G.190 Water bridges: B:G.13, B:G.19, B:G.19, B:D.37 NAD.8: 28 residues within 4Å: Chain C: G.13, A.15, Q.16, G.17, I.18, D.37, I.38, A.59, D.60, I.61, N.87, A.88, S.89, V.91, V.110, I.138, A.139, S.140, Y.153, K.157, P.183, G.184, L.185, I.186, S.188, G.190, V.191 Ligands: 4PL.9 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:P.183 Hydrogen bonds: C:Q.16, C:Q.16, C:I.18, C:I.38, C:D.60, C:I.61, C:N.87, C:K.157, C:I.186, C:I.186, C:S.188, C:S.188, C:G.190 Water bridges: C:G.13, C:G.19, C:G.19, C:D.37 NAD.11: 28 residues within 4Å: Chain D: G.13, A.15, Q.16, G.17, I.18, D.37, I.38, A.59, D.60, I.61, N.87, A.88, S.89, V.91, V.110, I.138, A.139, S.140, Y.153, K.157, P.183, G.184, L.185, I.186, S.188, G.190, V.191 Ligands: 4PL.12 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:P.183 Hydrogen bonds: D:Q.16, D:I.18, D:I.38, D:D.60, D:D.60, D:I.61, D:N.87, D:S.89, D:Y.153, D:K.157, D:I.186, D:I.186, D:S.188, D:S.188, D:G.190 Water bridges: D:G.19, D:G.19, D:D.37

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

4PL.2: 11 residues within 4Å: Chain A: V.91, S.140, N.141, T.142, M.150, Y.153, P.183, L.185, H.196, M.244 Ligands: NAD.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.142, A:L.185 Hydrogen bonds: A:S.140, A:N.141, A:T.142 pi-Stacking: A:H.196 4PL.7: 11 residues within 4Å: Chain B: V.91, S.140, N.141, T.142, M.150, Y.153, P.183, L.185, H.196, M.244 Ligands: NAD.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.142, B:L.185 Hydrogen bonds: B:N.141, B:T.142, B:Y.153 pi-Stacking: B:H.196 4PL.9: 11 residues within 4Å: Chain C: V.91, S.140, N.141, T.142, M.150, Y.153, P.183, L.185, H.196, M.244 Ligands: NAD.8 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:T.142, C:L.185 Hydrogen bonds: C:N.141, C:T.142, C:Y.153 pi-Stacking: C:H.196 4PL.12: 11 residues within 4Å: Chain D: V.91, S.140, N.141, T.142, M.150, Y.153, P.183, L.185, H.196, M.244 Ligands: NAD.11 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:T.142, D:L.185 Hydrogen bonds: D:N.141, D:T.142 pi-Stacking: D:H.196

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: I.90, P.92, H.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.103 Water bridges: A:D.102 GOL.4: 2 residues within 4Å: Chain A: R.246 Chain B: R.246 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:R.246, A:R.246 Water bridges: B:R.246, D:R.165, C:R.165, A:R.246 GOL.5: 3 residues within 4Å: Chain A: R.231 Chain C: E.216, H.217 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.231, A:R.231 Water bridges: A:R.231, C:H.217 GOL.10: 4 residues within 4Å: Chain C: V.94, D.98, D.100, H.103 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.100, C:H.103 GOL.13: 4 residues within 4Å: Chain B: Q.214, E.216, H.217 Chain D: R.231 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:E.216, D:R.231, D:R.231 Water bridges: B:Q.214, B:Q.214, B:Q.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yagi, T. et al., Crystal structure of complex of 4PAL (4-Pyridoxolactone) and PLDH (tetrameric pyridoxal 4-dehydrogenase) from Mesorhizobium loti. TO BE PUBLISHED

Release Date

2012-05-09

Peptides

Pyridoxal 4-dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyridoxal 4-dehydrogenase

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