SMTL ID : 4o84.2 (1 other biounit)

SAICAR synthetase (Type-1) in complex with GMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-hexamer

Ligands

42 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.1: 5 residues within 4Å: Chain A: E.158, D.162 Chain B: E.158, K.161, D.162 Ligand excluded by PLIP CD.2: 2 residues within 4Å: Chain A: H.63 Chain B: E.111 Ligand excluded by PLIP CD.3: 4 residues within 4Å: Chain A: E.89, D.124, D.128 Ligands: 5GP.8 Ligand excluded by PLIP CD.4: 2 residues within 4Å: Chain A: D.35, H.127 Ligand excluded by PLIP CD.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CD.6: 1 residues within 4Å: Chain A: E.226 Ligand excluded by PLIP CD.7: 3 residues within 4Å: Chain A: E.89, D.128 Ligands: 5GP.8 Ligand excluded by PLIP CD.11: 2 residues within 4Å: Chain A: E.111 Chain B: H.63 Ligand excluded by PLIP CD.12: 3 residues within 4Å: Chain B: E.89, D.128 Ligands: 5GP.18 Ligand excluded by PLIP CD.13: 2 residues within 4Å: Chain B: D.35, H.127 Ligand excluded by PLIP CD.14: 2 residues within 4Å: Chain B: E.81, D.181 Ligand excluded by PLIP CD.15: 1 residues within 4Å: Chain B: E.125 Ligand excluded by PLIP CD.16: 2 residues within 4Å: Chain B: E.226, E.229 Ligand excluded by PLIP CD.17: 3 residues within 4Å: Chain B: E.89, D.128 Ligands: 5GP.18 Ligand excluded by PLIP CD.21: 5 residues within 4Å: Chain C: E.158, D.162 Chain D: E.158, K.161, D.162 Ligand excluded by PLIP CD.22: 2 residues within 4Å: Chain C: H.63 Chain D: E.111 Ligand excluded by PLIP CD.23: 4 residues within 4Å: Chain C: E.89, D.124, D.128 Ligands: 5GP.28 Ligand excluded by PLIP CD.24: 2 residues within 4Å: Chain C: D.35, H.127 Ligand excluded by PLIP CD.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CD.26: 1 residues within 4Å: Chain C: E.226 Ligand excluded by PLIP CD.27: 3 residues within 4Å: Chain C: E.89, D.128 Ligands: 5GP.28 Ligand excluded by PLIP CD.31: 2 residues within 4Å: Chain C: E.111 Chain D: H.63 Ligand excluded by PLIP CD.32: 3 residues within 4Å: Chain D: E.89, D.128 Ligands: 5GP.38 Ligand excluded by PLIP CD.33: 2 residues within 4Å: Chain D: D.35, H.127 Ligand excluded by PLIP CD.34: 2 residues within 4Å: Chain D: E.81, D.181 Ligand excluded by PLIP CD.35: 1 residues within 4Å: Chain D: E.125 Ligand excluded by PLIP CD.36: 2 residues within 4Å: Chain D: E.226, E.229 Ligand excluded by PLIP CD.37: 3 residues within 4Å: Chain D: E.89, D.128 Ligands: 5GP.38 Ligand excluded by PLIP CD.41: 5 residues within 4Å: Chain E: E.158, D.162 Chain F: E.158, K.161, D.162 Ligand excluded by PLIP CD.42: 2 residues within 4Å: Chain E: H.63 Chain F: E.111 Ligand excluded by PLIP CD.43: 4 residues within 4Å: Chain E: E.89, D.124, D.128 Ligands: 5GP.48 Ligand excluded by PLIP CD.44: 2 residues within 4Å: Chain E: D.35, H.127 Ligand excluded by PLIP CD.45: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CD.46: 1 residues within 4Å: Chain E: E.226 Ligand excluded by PLIP CD.47: 3 residues within 4Å: Chain E: E.89, D.128 Ligands: 5GP.48 Ligand excluded by PLIP CD.51: 2 residues within 4Å: Chain E: E.111 Chain F: H.63 Ligand excluded by PLIP CD.52: 3 residues within 4Å: Chain F: E.89, D.128 Ligands: 5GP.58 Ligand excluded by PLIP CD.53: 2 residues within 4Å: Chain F: D.35, H.127 Ligand excluded by PLIP CD.54: 2 residues within 4Å: Chain F: E.81, D.181 Ligand excluded by PLIP CD.55: 1 residues within 4Å: Chain F: E.125 Ligand excluded by PLIP CD.56: 2 residues within 4Å: Chain F: E.226, E.229 Ligand excluded by PLIP CD.57: 3 residues within 4Å: Chain F: E.89, D.128 Ligands: 5GP.58 Ligand excluded by PLIP

6 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.8: 17 residues within 4Å: Chain A: E.89, V.91, R.93, G.98, S.99, D.128, D.173, F.174, K.175, D.195, T.196, C.197, R.198, R.214 Ligands: CD.3, CD.7, PO4.9 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.99, A:S.99, A:D.128, A:D.173, A:D.195, A:R.214, A:R.214 Water bridges: A:K.175, A:D.195, A:C.197 Salt bridges: A:R.93, A:R.198 pi-Cation interactions: A:K.175 5GP.18: 19 residues within 4Å: Chain B: E.89, V.91, R.93, G.98, S.99, Y.120, D.128, D.173, F.174, K.175, D.195, T.196, C.197, R.198, K.210, R.214 Ligands: CD.12, CD.17, PO4.19 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.99, B:S.99, B:S.99, B:D.173, B:D.195, B:K.210, B:R.214, B:R.214 Salt bridges: B:R.93, B:R.198 pi-Cation interactions: B:K.175 5GP.28: 17 residues within 4Å: Chain C: E.89, V.91, R.93, G.98, S.99, D.128, D.173, F.174, K.175, D.195, T.196, C.197, R.198, R.214 Ligands: CD.23, CD.27, PO4.29 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.99, C:S.99, C:D.128, C:D.173, C:D.195, C:R.214, C:R.214 Water bridges: C:K.175, C:D.195, C:C.197 Salt bridges: C:R.93, C:R.198 pi-Cation interactions: C:K.175 5GP.38: 19 residues within 4Å: Chain D: E.89, V.91, R.93, G.98, S.99, Y.120, D.128, D.173, F.174, K.175, D.195, T.196, C.197, R.198, K.210, R.214 Ligands: CD.32, CD.37, PO4.39 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.99, D:S.99, D:S.99, D:D.173, D:D.195, D:K.210, D:R.214, D:R.214 Salt bridges: D:R.93, D:R.198 pi-Cation interactions: D:K.175 5GP.48: 17 residues within 4Å: Chain E: E.89, V.91, R.93, G.98, S.99, D.128, D.173, F.174, K.175, D.195, T.196, C.197, R.198, R.214 Ligands: CD.43, CD.47, PO4.49 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:S.99, E:S.99, E:D.128, E:D.173, E:D.195, E:R.214, E:R.214 Water bridges: E:K.175, E:D.195, E:C.197 Salt bridges: E:R.93, E:R.198 pi-Cation interactions: E:K.175 5GP.58: 19 residues within 4Å: Chain F: E.89, V.91, R.93, G.98, S.99, Y.120, D.128, D.173, F.174, K.175, D.195, T.196, C.197, R.198, K.210, R.214 Ligands: CD.52, CD.57, PO4.59 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.99, F:S.99, F:S.99, F:D.173, F:D.195, F:K.210, F:R.214, F:R.214 Salt bridges: F:R.93, F:R.198 pi-Cation interactions: F:K.175

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 5 residues within 4Å: Chain A: T.32, A.33, K.210, R.214 Ligands: 5GP.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.34 Water bridges: A:D.35 Salt bridges: A:K.210, A:R.214 PO4.19: 5 residues within 4Å: Chain B: T.32, A.33, K.210, R.214 Ligands: 5GP.18 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.210, B:R.214 PO4.29: 5 residues within 4Å: Chain C: T.32, A.33, K.210, R.214 Ligands: 5GP.28 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.34 Water bridges: C:D.35 Salt bridges: C:K.210, C:R.214 PO4.39: 5 residues within 4Å: Chain D: T.32, A.33, K.210, R.214 Ligands: 5GP.38 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.210, D:R.214 PO4.49: 5 residues within 4Å: Chain E: T.32, A.33, K.210, R.214 Ligands: 5GP.48 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:F.34 Water bridges: E:D.35 Salt bridges: E:K.210, E:R.214 PO4.59: 5 residues within 4Å: Chain F: T.32, A.33, K.210, R.214 Ligands: 5GP.58 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:K.210, F:R.214

6 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.10: 5 residues within 4Å: Chain A: Y.133, Y.134, K.137, L.143 Chain D: Y.133 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:Y.133, A:Y.134, A:L.143 Water bridges: A:Y.134, D:E.114 Hydrogen bonds: D:Y.133 BU1.20: 3 residues within 4Å: Chain B: Y.133, Y.134 Chain E: Y.133 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.133, B:Y.134, B:Y.134 Hydrogen bonds: B:Y.133 BU1.30: 5 residues within 4Å: Chain C: Y.133, Y.134, K.137, L.143 Chain F: Y.133 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain C Hydrogen bonds: F:Y.133 Water bridges: F:E.114, C:Y.134 Hydrophobic interactions: C:Y.133, C:Y.134, C:L.143 BU1.40: 3 residues within 4Å: Chain A: Y.133 Chain D: Y.133, Y.134 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.133, D:Y.134, D:Y.134 Hydrogen bonds: D:Y.133 BU1.50: 5 residues within 4Å: Chain B: Y.133 Chain E: Y.133, Y.134, K.137, L.143 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:Y.133 Water bridges: B:E.114, E:Y.134 Hydrophobic interactions: E:Y.133, E:Y.134, E:L.143 BU1.60: 3 residues within 4Å: Chain C: Y.133 Chain F: Y.133, Y.134 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:Y.133, F:Y.134, F:Y.134 Hydrogen bonds: F:Y.133 Water bridges: F:Y.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manjunath, K. et al., SAICAR synthetase (Type-1) in complex with GMP. To be Published

Release Date

2014-12-31

Peptides

Phosphoribosylaminoimidazole-succinocarboxamide synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Phosphoribosylaminoimidazole-succinocarboxamide synthase

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