SMTL ID : 1qrr.1

CRYSTAL STRUCTURE OF SQD1 PROTEIN COMPLEX WITH NAD AND UDP-GLUCOSE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: F.294, E.296, Q.297, H.339 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.297, A:Q.297 Water bridges: A:A.337 Salt bridges: A:H.339 SO4.2: 3 residues within 4Å: Chain A: H.20, K.23, K.24 7 PLIP interactions: 7 interactions with chain A Water bridges: A:H.20, A:H.20, A:K.23, A:K.24 Salt bridges: A:H.20, A:K.23, A:K.24 SO4.5: 4 residues within 4Å: Chain B: F.294, E.296, Q.297, H.339 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.297, B:Q.297 Water bridges: B:A.337 Salt bridges: B:H.339 SO4.6: 3 residues within 4Å: Chain B: H.20, K.23, K.24 7 PLIP interactions: 7 interactions with chain B Water bridges: B:H.20, B:H.20, B:K.23, B:K.24 Salt bridges: B:H.20, B:K.23, B:K.24

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

NAD.3: 26 residues within 4Å: Chain A: G.8, D.10, G.11, Y.12, C.13, D.32, N.33, L.34, V.35, R.36, G.74, D.75, I.76, F.97, G.98, E.99, R.101, N.119, L.143, Y.182, K.186, Q.209, G.210, V.212, T.238 Ligands: UPG.4 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:Q.209, A:V.212 Hydrogen bonds: A:Y.12, A:C.13, A:G.14, A:N.33, A:N.33, A:L.34, A:V.35, A:R.36, A:D.75, A:I.76, A:E.99, A:R.101, A:N.119, A:K.186, A:V.212 Water bridges: A:D.10, A:G.11, A:R.36, A:R.37, A:F.97, A:E.99, A:R.101, A:R.101, A:R.101, A:Y.115 Salt bridges: A:R.36, A:R.101, A:R.101 NAD.7: 26 residues within 4Å: Chain B: G.8, D.10, G.11, Y.12, C.13, D.32, N.33, L.34, V.35, R.36, G.74, D.75, I.76, F.97, G.98, E.99, R.101, N.119, L.143, Y.182, K.186, Q.209, G.210, V.212, T.238 Ligands: UPG.8 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:Q.209, B:V.212 Hydrogen bonds: B:Y.12, B:C.13, B:G.14, B:N.33, B:N.33, B:L.34, B:V.35, B:R.36, B:D.75, B:I.76, B:E.99, B:R.101, B:N.119, B:K.186, B:V.212 Water bridges: B:D.10, B:G.11, B:R.36, B:R.37, B:F.97, B:E.99, B:R.101, B:R.101, B:R.101, B:Y.115 Salt bridges: B:R.36, B:R.101, B:R.101

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

UPG.4: 23 residues within 4Å: Chain A: R.101, A.103, T.145, M.146, G.147, Y.182, H.183, Q.209, G.210, V.211, T.238, A.239, R.242, F.243, T.254, V.255, Y.256, Q.261, R.263, V.300, R.327, E.329 Ligands: NAD.3 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:R.101, A:R.101, A:T.145, A:M.146, A:G.147, A:Y.182, A:Y.182, A:Q.209, A:A.239, A:R.242, A:T.254, A:T.254, A:Y.256, A:Q.261, A:E.329 Water bridges: A:F.236, A:R.263, A:R.327, A:R.327, A:R.327 Salt bridges: A:H.183, A:H.183, A:R.327, A:R.327 pi-Stacking: A:Y.256 UPG.8: 23 residues within 4Å: Chain B: R.101, A.103, T.145, M.146, G.147, Y.182, H.183, Q.209, G.210, V.211, T.238, A.239, R.242, F.243, T.254, V.255, Y.256, Q.261, R.263, V.300, R.327, E.329 Ligands: NAD.7 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:R.101, B:R.101, B:T.145, B:M.146, B:G.147, B:Y.182, B:Y.182, B:Q.209, B:A.239, B:R.242, B:T.254, B:T.254, B:Y.256, B:Q.261, B:E.329 Water bridges: B:F.236, B:R.263, B:R.327, B:R.327, B:R.327 Salt bridges: B:H.183, B:H.183, B:R.327, B:R.327 pi-Stacking: B:Y.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mulichak, A.M. et al., Crystal structure of SQD1, an enzyme involved in the biosynthesis of the plant sulfolipid headgroup donor UDP-sulfoquinovose. Proc.Natl.Acad.Sci.USA (1999)

Release Date

1999-11-10

Peptides

sulfolipid biosynthesis (SQD1) PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

sulfolipid biosynthesis (SQD1) PROTEIN