SMTL ID : 7x2y.1

Crystal Structure of cis-4,5-dihydrodiol phthalate dehydrogenase in complex with NAD+ and 3-Hydroxybenzoate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 3 residues within 4Å: Chain A: L.25, Q.26, L.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.33 PEG.3: 5 residues within 4Å: Chain A: L.14, T.19, R.40, A.43 Ligands: GOL.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.16 PEG.10: 2 residues within 4Å: Chain B: R.16, T.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.16 PEG.12: 4 residues within 4Å: Chain B: L.25, Q.26, K.32, L.33 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.33, B:L.33 PEG.14: 6 residues within 4Å: Chain B: A.63, S.64, N.65, P.66, H.90, K.92 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.65, B:K.92 PEG.15: 5 residues within 4Å: Chain B: R.198, R.199, E.224, G.225, E.389 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.199, B:G.225 Water bridges: B:E.389

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: L.14, F.18, A.43, Q.46, F.47, D.50, F.51 Ligands: PEG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.43, A:D.50 GOL.5: 5 residues within 4Å: Chain A: H.77, Q.78, L.102, S.103, D.106 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.78, A:L.102, A:S.103, A:S.103 Water bridges: A:D.106, A:D.106 GOL.8: 5 residues within 4Å: Chain A: R.190, G.194, T.195, R.196, W.367 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.190, A:R.190 Water bridges: A:R.190, A:V.197 GOL.9: 6 residues within 4Å: Chain B: F.18, A.43, Q.46, F.47, D.50, F.51 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.43 GOL.13: 7 residues within 4Å: Chain B: Y.156, T.157, D.158, G.237, H.238, F.239, D.240 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.157 Water bridges: B:H.238, B:S.241

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 5 residues within 4Å: Chain A: R.115, H.120, L.121, P.361, D.364 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.115, A:L.121, A:L.121, A:L.121 Water bridges: A:G.365 Salt bridges: A:H.120 PO4.11: 4 residues within 4Å: Chain B: D.242, G.249, E.250, K.255 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.242, B:E.250 Water bridges: B:D.158, B:G.249 Salt bridges: B:K.255

2 x 3HB: 3-HYDROXYBENZOIC ACID(Non-covalent)

3HB.6: 12 residues within 4Å: Chain A: L.20, E.97, H.125, R.164, E.167, S.180, Q.181, H.184, E.250, M.251, R.344 Ligands: NAD.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.20 Hydrogen bonds: A:S.180, A:Q.181 Water bridges: A:R.344 Salt bridges: A:H.125, A:H.184, A:R.344 3HB.16: 11 residues within 4Å: Chain B: L.20, E.97, H.125, E.167, S.180, Q.181, H.184, E.250, M.251, R.344 Ligands: NAD.17 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.125, B:S.180, B:Q.181 Water bridges: B:R.344, B:R.344 Salt bridges: B:H.125, B:R.344

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

NAD.7: 22 residues within 4Å: Chain A: G.13, G.15, R.16, A.17, L.20, D.38, P.39, R.40, A.74, S.75, P.76, H.77, F.79, Q.83, E.97, K.98, P.99, R.164, R.165, P.166, E.167 Ligands: 3HB.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.17 Hydrogen bonds: A:R.16, A:A.17, A:R.40, A:H.77, A:Q.83, A:E.167 Salt bridges: A:R.165 NAD.17: 22 residues within 4Å: Chain B: G.13, G.15, R.16, A.17, L.20, D.38, P.39, R.40, A.74, S.75, P.76, H.77, F.79, Q.83, E.97, K.98, P.99, R.164, R.165, P.166, E.167 Ligands: 3HB.16 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.17 Hydrogen bonds: B:R.16, B:A.17, B:R.40, B:H.77, B:Q.83, B:R.164 Water bridges: B:G.15, B:F.18, B:Q.82 Salt bridges: B:R.165 pi-Stacking: B:F.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mahto, J.K. et al., Conformational flexibility enables catalysis of phthalate cis-4,5-dihydrodiol dehydrogenase. Arch.Biochem.Biophys. (2022)

Release Date

2022-09-14

Peptides

4,5-dihydroxyphthalate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

4,5-dihydroxyphthalate dehydrogenase

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