SMTL ID : 7xgl.1

Quinolinate Phosphoribosyl Transferase (QAPRTase) from Streptomyces pyridomyceticus NRRL B-2517 in Apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.152, G.282, A.283, H.286 Ligands: GOL.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.282, A:A.283 Water bridges: A:G.261, A:G.261, A:G.261 Salt bridges: A:K.152, A:H.286 SO4.2: 8 residues within 4Å: Chain A: S.150, R.151, H.173, R.174, L.182, K.184 Ligands: SO4.3, GOL.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.151 Water bridges: A:K.184 Salt bridges: A:R.151, A:H.173, A:R.174, A:K.184 SO4.3: 5 residues within 4Å: Chain A: R.151, K.184 Chain B: E.116, R.117 Ligands: SO4.2 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Water bridges: A:K.184, B:R.117, B:R.117, B:R.117, B:R.117 Salt bridges: A:R.151, A:K.184, B:R.117 Hydrogen bonds: B:E.116, B:E.116 SO4.11: 3 residues within 4Å: Chain A: K.152 Chain B: R.61, R.117 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.292 Water bridges: B:R.61 Salt bridges: B:R.61, B:R.117, A:K.152 SO4.12: 7 residues within 4Å: Chain B: K.152, G.261, G.262, V.281, G.282, H.286 Ligands: GOL.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.262, B:G.282 Water bridges: B:G.261, B:G.261, B:A.283, B:A.283 Salt bridges: B:K.152, B:H.286 SO4.13: 7 residues within 4Å: Chain B: R.148, S.150, R.151, R.174, L.182, K.184 Ligands: GOL.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.151 Water bridges: B:S.150, B:R.174, B:K.184 Salt bridges: B:R.148, B:R.151, B:R.174, B:K.184

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: S.150, K.152, K.184, M.232, S.260, A.280, G.282 Ligands: SO4.1, SO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.184, A:K.184, A:S.260, A:G.282 Water bridges: A:G.261 GOL.8: 10 residues within 4Å: Chain B: R.148, K.152, K.184, M.232, S.260, A.280, G.282 Ligands: 0L1.5, SO4.12, SO4.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.148, B:R.148, B:K.152, B:K.184, B:K.184, B:G.282 GOL.9: 7 residues within 4Å: Chain A: L.113, E.116 Chain B: K.184, D.185, N.186, E.213 Ligands: 0L1.5 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.185, B:D.185, B:D.185, B:N.186, B:N.186 Water bridges: A:L.113, A:E.116, A:L.295

1 x 0L1: hexanedioic acid(Non-covalent)

0L1.5: 7 residues within 4Å: Chain A: E.116, R.117 Chain B: R.151, K.152, K.184 Ligands: GOL.8, GOL.9 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Water bridges: A:R.61, A:E.116, A:R.117, A:R.117, B:R.151 Salt bridges: A:R.117, A:R.117, B:R.151, B:K.152, B:K.184 Hydrophobic interactions: B:K.184

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: R.166, R.167 Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: R.166, R.167 Ligand excluded by PLIP

1 x 144: TRIS-HYDROXYMETHYL-METHYL-AMMONIUM(Non-covalent)

144.10: 13 residues within 4Å: Chain A: H.125, L.154, T.285, H.286, S.287, A.288 Chain B: H.125, L.154, T.285, H.286, S.287, A.288, P.289 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.285, A:A.288, B:T.285, B:A.288 Water bridges: A:S.287, B:S.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Z. et al., Bifunctional NadC Homologue PyrZ Catalyzes Nicotinic Acid Formation in Pyridomycin Biosynthesis. Acs Chem.Biol. (2023)

Release Date

2023-03-22

Peptides

Quinolinate Phosphoribosyl Transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Quinolinate Phosphoribosyl Transferase

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