SMTL ID : 6tak.1

Crystal structure of Escherichia coli Orotate Phosphoribosyltransferase in complex with Orotic acid and Sulfate at 1.25 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

2 x ORO: OROTIC ACID(Non-covalent)

ORO.1: 9 residues within 4Å: Chain A: L.25, K.26, F.34, F.35, N.36, V.126, T.128, R.156 Ligands: SO4.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.25 Hydrogen bonds: A:K.26, A:F.35, A:F.35, A:R.156 Water bridges: A:S.27, A:D.125 pi-Stacking: A:F.34 ORO.9: 8 residues within 4Å: Chain B: L.25, K.26, F.34, F.35, N.36, V.126, T.128, R.156 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:T.128 Hydrogen bonds: B:K.26, B:F.35, B:F.35, B:R.156 Water bridges: B:S.27, B:R.156, B:E.158 pi-Stacking: B:F.34

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.29, R.159, G.160, R.161, F.211 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.29, A:R.29, A:R.159 Water bridges: A:G.160 GOL.7: 5 residues within 4Å: Chain A: I.62, E.63, F.64, L.91, L.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.64 GOL.10: 6 residues within 4Å: Chain B: I.62, E.63, F.64, L.91, L.93, R.119 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.64 Water bridges: B:F.64, B:D.65 GOL.15: 4 residues within 4Å: Chain B: K.185, I.188, K.205, R.208 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.208, B:R.208 Water bridges: B:K.185, B:K.185, B:K.205 GOL.16: 4 residues within 4Å: Chain B: Q.157, T.183, K.185, D.186 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.183, B:D.186, B:D.186 GOL.17: 4 residues within 4Å: Chain B: R.51, E.55, H.88, H.89 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.51, B:R.51 Water bridges: B:R.51, B:E.55

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

SO4.3: 5 residues within 4Å: Chain A: R.99 Chain B: A.71, Y.72, K.73, K.100 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:R.99, A:R.99 Salt bridges: A:R.99 Hydrogen bonds: B:Y.72, B:K.73 SO4.4: 7 residues within 4Å: Chain A: A.71, Y.72, K.73, K.100 Chain B: R.99, K.103 Ligands: SO4.11 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.72, A:K.73 Water bridges: A:A.71 Salt bridges: A:K.73, A:K.100, B:R.99, B:K.103 SO4.5: 8 residues within 4Å: Chain A: K.26, I.127, T.128, A.129, G.130, T.131, A.132, I.133 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.128, A:T.128, A:A.129, A:G.130, A:T.131, A:T.131, A:A.132 Salt bridges: A:K.26 SO4.6: 3 residues within 4Å: Chain A: F.11, K.15, R.44 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.14 Salt bridges: A:K.15, A:R.44 SO4.8: 6 residues within 4Å: Chain A: K.26, F.34, K.73 Chain B: K.103, H.105 Ligands: ORO.1 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:K.73, B:K.103, B:H.105 Hydrogen bonds: B:H.105 SO4.11: 5 residues within 4Å: Chain A: K.100 Chain B: K.103, D.104, H.105 Ligands: SO4.4 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.104, B:H.105 Water bridges: B:D.104, A:K.100 Salt bridges: B:K.103, A:K.100 SO4.12: 3 residues within 4Å: Chain B: K.15, R.44, L.48 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.15 Salt bridges: B:K.15, B:R.44 SO4.13: 3 residues within 4Å: Chain B: R.44, L.48, R.51 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.44, B:R.51 SO4.14: 10 residues within 4Å: Chain B: K.73, D.124, V.126, I.127, T.128, A.129, G.130, T.131, A.132, I.133 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:D.124, B:T.128, B:A.129, B:G.130, B:T.131, B:A.132, B:I.133 Water bridges: B:K.26, B:K.26, B:K.73, B:K.73, B:T.128 Salt bridges: B:K.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roca, M. et al., Elucidating the Catalytic Reaction Mechanism of Orotate Phosphoribosyltransferase by Means of X-ray Crystallography and Computational Simulations. Acs Catalysis (2020)

Release Date

2020-11-25

Peptides

Orotate phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Orotate phosphoribosyltransferase

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