SMTL ID : 1i2b.2 (1 other biounit)

CRYSTAL STRUCTURE OF MUTANT T145A SQD1 PROTEIN COMPLEX WITH NAD AND UDP-SULFOQUINOVOSE/UDP-GLUCOSE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: F.304, E.306, Q.307, H.349 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.307 Water bridges: A:Q.307, A:Q.307, A:A.347 Salt bridges: A:H.349 SO4.2: 3 residues within 4Å: Chain A: H.30, K.33, K.34 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.33, A:K.33, A:K.33 Salt bridges: A:H.30, A:K.33, A:K.34 SO4.6: 4 residues within 4Å: Chain B: F.304, E.306, Q.307, H.349 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.307 Water bridges: B:Q.307, B:Q.307, B:A.347 Salt bridges: B:H.349 SO4.7: 3 residues within 4Å: Chain B: H.30, K.33, K.34 6 PLIP interactions: 6 interactions with chain B Water bridges: B:K.33, B:K.33, B:K.33 Salt bridges: B:H.30, B:K.33, B:K.34 SO4.11: 4 residues within 4Å: Chain C: F.304, E.306, Q.307, H.349 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.307 Water bridges: C:Q.307, C:Q.307, C:A.347 Salt bridges: C:H.349 SO4.12: 3 residues within 4Å: Chain C: H.30, K.33, K.34 6 PLIP interactions: 6 interactions with chain C Water bridges: C:K.33, C:K.33, C:K.33 Salt bridges: C:H.30, C:K.33, C:K.34 SO4.16: 4 residues within 4Å: Chain D: F.304, E.306, Q.307, H.349 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.307 Water bridges: D:Q.307, D:Q.307, D:A.347 Salt bridges: D:H.349 SO4.17: 3 residues within 4Å: Chain D: H.30, K.33, K.34 6 PLIP interactions: 6 interactions with chain D Water bridges: D:K.33, D:K.33, D:K.33 Salt bridges: D:H.30, D:K.33, D:K.34

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

NAD.3: 26 residues within 4Å: Chain A: G.18, D.20, G.21, Y.22, C.23, D.42, N.43, L.44, V.45, R.46, G.84, D.85, I.86, F.107, G.108, E.109, R.111, N.129, L.153, Y.192, K.196, Q.219, G.220, V.222 Ligands: UPG.4, USQ.5 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:Q.219, A:V.222 Hydrogen bonds: A:G.18, A:Y.22, A:C.23, A:G.24, A:N.43, A:L.44, A:V.45, A:R.46, A:I.86, A:E.109, A:N.129, A:N.129, A:K.196, A:V.222 Water bridges: A:D.20, A:G.21, A:R.46, A:R.47, A:F.107, A:E.109, A:R.111, A:R.111, A:Y.125, A:F.246, A:T.248 Salt bridges: A:R.111, A:R.111 NAD.8: 26 residues within 4Å: Chain B: G.18, D.20, G.21, Y.22, C.23, D.42, N.43, L.44, V.45, R.46, G.84, D.85, I.86, F.107, G.108, E.109, R.111, N.129, L.153, Y.192, K.196, Q.219, G.220, V.222 Ligands: UPG.9, USQ.10 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:Q.219, B:V.222 Hydrogen bonds: B:G.18, B:Y.22, B:C.23, B:G.24, B:N.43, B:L.44, B:V.45, B:R.46, B:D.85, B:I.86, B:E.109, B:N.129, B:N.129, B:Y.192, B:K.196, B:V.222 Water bridges: B:G.21, B:D.42, B:R.46, B:R.47, B:F.107, B:E.109, B:R.111, B:R.111, B:F.246, B:T.248 Salt bridges: B:R.111, B:R.111 NAD.13: 26 residues within 4Å: Chain C: G.18, D.20, G.21, Y.22, C.23, D.42, N.43, L.44, V.45, R.46, G.84, D.85, I.86, F.107, G.108, E.109, R.111, N.129, L.153, Y.192, K.196, Q.219, G.220, V.222 Ligands: UPG.14, USQ.15 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:Q.219, C:V.222 Hydrogen bonds: C:G.18, C:Y.22, C:C.23, C:G.24, C:N.43, C:L.44, C:V.45, C:R.46, C:I.86, C:E.109, C:N.129, C:N.129, C:K.196, C:V.222 Water bridges: C:D.20, C:G.21, C:R.46, C:R.47, C:F.107, C:E.109, C:R.111, C:R.111, C:Y.125, C:F.246, C:T.248 Salt bridges: C:R.111, C:R.111 NAD.18: 26 residues within 4Å: Chain D: G.18, D.20, G.21, Y.22, C.23, D.42, N.43, L.44, V.45, R.46, G.84, D.85, I.86, F.107, G.108, E.109, R.111, N.129, L.153, Y.192, K.196, Q.219, G.220, V.222 Ligands: UPG.19, USQ.20 30 PLIP interactions: 30 interactions with chain D Hydrophobic interactions: D:Q.219, D:V.222 Hydrogen bonds: D:G.18, D:Y.22, D:C.23, D:G.24, D:N.43, D:L.44, D:V.45, D:R.46, D:D.85, D:I.86, D:E.109, D:N.129, D:N.129, D:Y.192, D:K.196, D:V.222 Water bridges: D:G.21, D:D.42, D:R.46, D:R.47, D:F.107, D:E.109, D:R.111, D:R.111, D:F.246, D:T.248 Salt bridges: D:R.111, D:R.111

4 x UPG: URIDINE-5'-DIPHOSPHATE-GLUCOSE(Non-covalent)

UPG.4: 23 residues within 4Å: Chain A: R.111, A.113, A.155, M.156, G.157, Y.192, H.193, Q.219, G.220, V.221, T.248, A.249, R.252, F.253, T.264, Y.266, Q.271, R.273, V.310, R.337, E.339 Ligands: NAD.3, USQ.5 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:R.111, A:R.111, A:M.156, A:G.157, A:Y.192, A:Y.192, A:Q.219, A:A.249, A:R.252, A:T.264, A:T.264, A:Y.266, A:Q.271, A:E.339 Water bridges: A:F.246, A:R.337, A:R.337, A:R.337 Salt bridges: A:H.193, A:H.193, A:R.337, A:R.337 pi-Stacking: A:Y.266 UPG.9: 23 residues within 4Å: Chain B: R.111, A.113, A.155, M.156, G.157, Y.192, H.193, Q.219, G.220, V.221, T.248, A.249, R.252, F.253, T.264, Y.266, Q.271, R.273, V.310, R.337, E.339 Ligands: NAD.8, USQ.10 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:R.111, B:R.111, B:M.156, B:G.157, B:Y.192, B:Q.219, B:A.249, B:R.252, B:T.264, B:Y.266, B:Q.271, B:E.339 Water bridges: B:F.246, B:R.337, B:R.337, B:R.337 Salt bridges: B:H.193, B:H.193, B:R.337, B:R.337 pi-Stacking: B:Y.266 UPG.14: 23 residues within 4Å: Chain C: R.111, A.113, A.155, M.156, G.157, Y.192, H.193, Q.219, G.220, V.221, T.248, A.249, R.252, F.253, T.264, Y.266, Q.271, R.273, V.310, R.337, E.339 Ligands: NAD.13, USQ.15 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:R.111, C:R.111, C:M.156, C:G.157, C:Y.192, C:Y.192, C:Q.219, C:A.249, C:R.252, C:T.264, C:T.264, C:Y.266, C:Q.271, C:E.339 Water bridges: C:F.246, C:R.337, C:R.337, C:R.337 Salt bridges: C:H.193, C:H.193, C:R.337, C:R.337 pi-Stacking: C:Y.266 UPG.19: 23 residues within 4Å: Chain D: R.111, A.113, A.155, M.156, G.157, Y.192, H.193, Q.219, G.220, V.221, T.248, A.249, R.252, F.253, T.264, Y.266, Q.271, R.273, V.310, R.337, E.339 Ligands: NAD.18, USQ.20 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:R.111, D:R.111, D:M.156, D:G.157, D:Y.192, D:Q.219, D:A.249, D:R.252, D:T.264, D:Y.266, D:Q.271, D:E.339 Water bridges: D:F.246, D:R.337, D:R.337, D:R.337 Salt bridges: D:H.193, D:H.193, D:R.337, D:R.337 pi-Stacking: D:Y.266

4 x USQ: SULFOQUINOVOSE-URIDINE-C1,5'-DIPHOSPHATE(Non-covalent)

USQ.5: 23 residues within 4Å: Chain A: R.111, A.113, A.155, M.156, G.157, Y.192, H.193, Q.219, G.220, V.221, T.248, A.249, R.252, F.253, T.264, Y.266, Q.271, R.273, V.310, R.337, E.339 Ligands: NAD.3, UPG.4 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:R.111, A:R.111, A:M.156, A:G.157, A:Y.192, A:Y.192, A:A.249, A:R.252, A:T.264, A:T.264, A:Y.266, A:Q.271, A:E.339 Water bridges: A:F.246, A:R.337, A:R.337, A:R.337 Salt bridges: A:H.193, A:H.193, A:H.193, A:R.337, A:R.337 pi-Stacking: A:Y.266 USQ.10: 23 residues within 4Å: Chain B: R.111, A.113, A.155, M.156, G.157, Y.192, H.193, Q.219, G.220, V.221, T.248, A.249, R.252, F.253, T.264, Y.266, Q.271, R.273, V.310, R.337, E.339 Ligands: NAD.8, UPG.9 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:R.111, B:R.111, B:M.156, B:G.157, B:Y.192, B:A.249, B:R.252, B:T.264, B:Y.266, B:Q.271, B:E.339 Water bridges: B:F.246, B:R.337, B:R.337, B:R.337 Salt bridges: B:H.193, B:H.193, B:H.193, B:R.337, B:R.337 pi-Stacking: B:Y.266 USQ.15: 23 residues within 4Å: Chain C: R.111, A.113, A.155, M.156, G.157, Y.192, H.193, Q.219, G.220, V.221, T.248, A.249, R.252, F.253, T.264, Y.266, Q.271, R.273, V.310, R.337, E.339 Ligands: NAD.13, UPG.14 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:R.111, C:R.111, C:M.156, C:G.157, C:Y.192, C:Y.192, C:A.249, C:R.252, C:T.264, C:T.264, C:Y.266, C:Q.271, C:E.339 Water bridges: C:F.246, C:R.337, C:R.337, C:R.337 Salt bridges: C:H.193, C:H.193, C:H.193, C:R.337, C:R.337 pi-Stacking: C:Y.266 USQ.20: 23 residues within 4Å: Chain D: R.111, A.113, A.155, M.156, G.157, Y.192, H.193, Q.219, G.220, V.221, T.248, A.249, R.252, F.253, T.264, Y.266, Q.271, R.273, V.310, R.337, E.339 Ligands: NAD.18, UPG.19 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:R.111, D:R.111, D:M.156, D:G.157, D:Y.192, D:A.249, D:R.252, D:T.264, D:Y.266, D:Q.271, D:E.339 Water bridges: D:F.246, D:R.337, D:R.337, D:R.337 Salt bridges: D:H.193, D:H.193, D:H.193, D:R.337, D:R.337 pi-Stacking: D:Y.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Theisen, M.J. et al., Characterization of the Active Site of UDP-sulfoquinovose Synthase: Formation of the Sulfonic Acid Product in the Crystalline State. To be Published

Release Date

2003-07-01

Peptides

SULFOLIPID BIOSYNTHESIS PROTEIN SQD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

SULFOLIPID BIOSYNTHESIS PROTEIN SQD1

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