SMTL ID : 4fe2.1

X-Ray Structure of SAICAR Synthetase (PurC) from Streptococcus pneumoniae complexed with AIR, ADP, Asp and Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-dimer

Ligands

2 x AIR: 5-AMINOIMIDAZOLE RIBONUCLEOTIDE(Non-covalent)

AIR.1: 15 residues within 4Å: Chain A: E.109, V.111, R.113, A.117, G.118, S.119, D.194, F.195, K.196, D.216, N.217, C.218, R.219, R.234 Ligands: ASP.6 13 PLIP interactions: 10 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:S.119, A:D.216, A:C.218, A:R.234, A:R.234, D.6, D.6 Water bridges: A:Y.140, A:C.218, A:C.218, D.6 Salt bridges: A:R.113, A:R.219 AIR.9: 13 residues within 4Å: Chain B: E.109, V.111, R.113, A.117, G.118, S.119, D.194, K.196, D.216, N.217, C.218, R.219, R.234 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.119, B:D.216, B:D.216, B:C.218, B:R.234, B:R.234 Water bridges: B:C.218, B:C.218, B:R.219 Salt bridges: B:R.113, B:R.219

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 17 residues within 4Å: Chain A: Y.27, G.29, K.30, A.31, K.32, I.34, H.88, K.101, K.102, V.103, I.105, K.142, E.198, A.210, D.211 Ligands: MG.3, ASP.6 20 PLIP interactions: 17 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:K.30, A:A.31, A:K.32, A:H.88, A:K.101, A:V.103, A:E.198, A:D.211, D.6, D.6 Water bridges: A:Y.27, A:K.32, A:K.142, A:K.142, A:K.142, A:E.212, D.6 Salt bridges: A:K.30, A:K.32, A:K.142 ADP.10: 15 residues within 4Å: Chain B: Y.27, G.29, K.30, A.31, K.32, I.34, H.88, K.101, K.102, V.103, I.105, E.198, A.210, D.211 Ligands: MG.11 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.30, B:A.31, B:K.32, B:K.101, B:V.103, B:E.198, B:D.211 Water bridges: B:K.32, B:K.32 Salt bridges: B:K.32, B:K.142

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 2 residues within 4Å: Ligands: ADP.2, ASP.6 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: ASP.6, H2O.4, H2O.5, H2O.5 MG.11: 1 residues within 4Å: Ligands: ADP.10 No protein-ligand interaction detected (PLIP)

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

144.4: 3 residues within 4Å: Chain A: N.81, V.82, G.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.82 Water bridges: A:N.81 144.7: 4 residues within 4Å: Chain A: A.83, G.84, E.173, R.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.84, A:E.173 Salt bridges: A:E.173 144.8: 6 residues within 4Å: Chain A: N.114, Y.115, A.131, L.132, E.133, K.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.133 Water bridges: A:E.133 144.12: 5 residues within 4Å: Chain A: K.122, R.123 Chain B: L.146, D.147, P.149 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.122, A:K.122, A:K.122, B:D.147

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

CL.5: 2 residues within 4Å: Chain A: R.123 Chain B: R.123 Ligand excluded by PLIP

1 x ASP: ASPARTIC ACID(Non-covalent)

ASP.6: 10 residues within 4Å: Chain A: K.30, E.109, K.142, D.148, K.196, D.211, N.217 Ligands: AIR.1, ADP.2, MG.3 10 PLIP interactions: 7 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:E.109, A:E.198, D.6, D.6 Water bridges: A:K.142, A:D.216, D.6 Salt bridges: A:K.30, A:K.142, A:K.196

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 4 residues within 4Å: Chain B: N.114, Y.115, A.131, L.132 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.114, B:Y.115 Hydrogen bonds: B:N.114, B:L.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wolf, N.M. et al., Structures of SAICAR synthetase (PurC) from Streptococcus pneumoniae with ADP, Mg(2+), AIR and Asp. Acta Crystallogr.,Sect.D (2014)

Release Date

2013-05-29

Peptides

Phosphoribosylaminoimidazole-succinocarboxamide synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphoribosylaminoimidazole-succinocarboxamide synthase

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