SMTL ID : 5tpr.1

Desmethyl-4-deoxygadusol synthase from Anabaena variabilis (Ava_3858) with NAD+ and Zn2+ bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.184, E.232, H.305, H.321, V.325 Ligands: NAD.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.232, A:H.305, A:H.321, H2O.1, H2O.10 ZN.8: 7 residues within 4Å: Chain B: D.184, E.232, K.235, H.305, H.321, V.325 Ligands: NAD.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.232, B:H.305, B:H.321, H2O.27

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

SO4.2: 9 residues within 4Å: Chain A: G.152, G.153, L.154, T.178, I.180, G.181, Q.225, N.228 Ligands: NAD.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.153, A:L.154, A:T.178, A:N.228 Water bridges: A:G.152, A:Q.225 SO4.4: 4 residues within 4Å: Chain A: K.190, N.200, H.305 Chain B: R.168 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.200 Water bridges: A:K.190, A:K.190, A:R.299, A:R.299 Salt bridges: A:K.190, B:R.168 SO4.5: 5 residues within 4Å: Chain A: L.198, R.201, S.377, L.380 Chain B: A.137 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Water bridges: A:R.201, A:R.201, A:R.201, A:E.376, B:R.167 Salt bridges: A:R.201 SO4.10: 5 residues within 4Å: Chain A: R.168 Chain B: K.190, N.200, H.305, P.309 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.200 Water bridges: B:R.299, B:R.299, B:R.299 Salt bridges: B:K.190, A:R.168 SO4.11: 5 residues within 4Å: Chain A: A.137 Chain B: L.198, R.201, S.377, L.380 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.377 Water bridges: B:R.201, B:R.201, B:R.201, B:R.201, A:K.140, A:K.140, A:R.167 Salt bridges: B:R.201 SO4.14: 9 residues within 4Å: Chain B: G.152, G.153, L.154, T.178, I.180, G.181, Q.225, N.228 Ligands: NAD.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.153, B:L.154, B:T.178, B:Q.225, B:N.228

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

NAD.3: 35 residues within 4Å: Chain A: D.90, N.92, V.93, L.96, Y.97, I.119, E.121, K.124, G.151, G.152, G.153, L.154, I.155, D.157, T.177, T.178, I.180, G.181, D.184, A.185, A.188, K.190, V.191, K.199, N.200, L.217, T.220, L.221, P.222, Q.225, N.228, E.232, H.321 Ligands: ZN.1, SO4.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.180, A:A.185 Hydrogen bonds: A:D.90, A:N.92, A:E.121, A:K.124, A:G.152, A:G.153, A:L.154, A:I.155, A:T.177, A:T.178, A:T.178, A:K.190, A:K.199, A:N.200, A:T.220, A:N.228 Water bridges: A:N.92, A:D.157, A:Q.225, A:Q.225 NAD.9: 37 residues within 4Å: Chain B: D.90, N.92, V.93, L.96, Y.97, I.119, E.121, K.124, G.151, G.152, G.153, L.154, I.155, D.157, T.177, T.178, I.180, G.181, D.184, A.185, A.188, K.190, V.191, K.199, N.200, L.217, T.220, L.221, P.222, Q.225, N.228, E.232, E.312, H.321, Y.435 Ligands: ZN.8, SO4.14 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:I.180, B:A.185 Hydrogen bonds: B:D.90, B:N.92, B:E.121, B:K.124, B:G.152, B:G.153, B:L.154, B:I.155, B:D.157, B:T.177, B:T.177, B:T.178, B:K.199, B:N.200, B:T.220, B:N.228 Water bridges: B:N.92, B:I.119, B:Q.225, B:Q.225, B:Q.225, B:Q.225, B:Q.225, B:Y.435

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

PEG.6: 5 residues within 4Å: Chain A: H.274, R.275, Y.278, K.279 Chain B: E.46 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.274, A:K.279, B:E.46 Water bridges: A:E.243 PEG.12: 7 residues within 4Å: Chain B: P.364, L.366, D.367, I.368, D.369, I.370, K.416 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.367, B:I.368, B:D.369, B:D.369 Water bridges: B:L.366

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: E.46 Chain B: H.274, R.275, Y.278, K.279 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:K.279 Hydrogen bonds: A:E.46 GOL.13: 6 residues within 4Å: Chain B: K.56, I.57, E.58, Y.59, A.207, R.209 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.58, B:A.207 Water bridges: B:K.56, B:A.207, B:A.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osborn, A.R. et al., Evolution and Distribution of C7-Cyclitol Synthases in Prokaryotes and Eukaryotes. ACS Chem. Biol. (2017)

Release Date

2017-02-22

Peptides

3-dehydroquinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3-dehydroquinate synthase