SMTL ID : 3zrr.1

Crystal structure and substrate specificity of a thermophilic archaeal serine : pyruvate aminotransferase from Sulfolobus solfataricus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

4 x PXG: 3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID(Non-covalent)

PXG.1: 19 residues within 4Å: Chain A: V.8, G.62, G.63, T.64, M.67, F.88, V.136, T.138, D.163, V.165, S.166, A.186, Q.188, K.189, R.337 Chain B: F.28, Y.240, A.242, T.243 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.88, A:F.88, A:T.138, A:V.165, A:V.165, B:F.28, B:Y.240 Hydrogen bonds: A:G.63, A:T.64, A:T.138, A:Q.188, A:Q.188, B:T.243, B:T.243, B:T.243 Water bridges: A:R.337, A:R.337 Salt bridges: A:R.337 pi-Stacking: A:F.88 pi-Cation interactions: A:K.189 PXG.5: 19 residues within 4Å: Chain A: F.28, Y.240, A.242, T.243 Chain B: V.8, G.62, G.63, T.64, M.67, F.88, V.136, T.138, D.163, V.165, S.166, A.186, Q.188, K.189, R.337 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.8, B:F.88, B:F.88, B:T.138, B:V.165, B:V.165, A:F.28, A:F.28 Hydrogen bonds: B:G.63, B:T.64, B:T.138, B:Q.188, A:T.243, A:T.243 Salt bridges: B:K.189, B:R.337 pi-Stacking: B:F.88, A:Y.240 pi-Cation interactions: B:K.189 PXG.7: 19 residues within 4Å: Chain C: V.8, G.62, G.63, T.64, M.67, F.88, V.136, T.138, D.163, V.165, S.166, A.186, Q.188, K.189, R.337 Chain D: F.28, Y.240, A.242, T.243 22 PLIP interactions: 17 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.88, C:F.88, C:T.138, C:V.165, C:V.165, D:F.28, D:Y.240 Hydrogen bonds: C:G.63, C:T.64, C:T.64, C:T.138, C:T.138, C:Q.188, C:Q.188, D:Y.240, D:T.243, D:T.243 Water bridges: C:R.337, C:R.337 Salt bridges: C:R.337 pi-Stacking: C:F.88 pi-Cation interactions: C:K.189 PXG.11: 19 residues within 4Å: Chain C: F.28, Y.240, A.242, T.243 Chain D: V.8, G.62, G.63, T.64, M.67, F.88, V.136, T.138, D.163, V.165, S.166, A.186, Q.188, K.189, R.337 21 PLIP interactions: 16 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:V.8, D:F.88, D:F.88, D:T.138, D:V.165, D:V.165, C:F.28, C:F.28 Hydrogen bonds: D:G.63, D:T.64, D:T.64, D:T.138, D:T.138, D:Q.188, C:Y.240, C:T.243 Salt bridges: D:K.189, D:R.337 pi-Stacking: D:F.88, C:Y.240 pi-Cation interactions: D:K.189

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: D.16 Chain C: E.23 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.16, C:E.23, H2O.1 CA.3: 1 residues within 4Å: Chain A: D.148 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.148, A:D.148 CA.4: 1 residues within 4Å: Chain A: E.288 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.288, A:E.288 CA.6: 2 residues within 4Å: Chain B: D.16 Chain D: E.23 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:D.16, B:D.16, D:E.23, H2O.13 CA.8: 2 residues within 4Å: Chain A: E.23 Chain C: D.16 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:D.16, C:D.16, A:E.23, H2O.20 CA.9: 1 residues within 4Å: Chain C: D.148 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.148, C:D.148 CA.10: 1 residues within 4Å: Chain C: E.288 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.288, C:E.288 CA.12: 2 residues within 4Å: Chain B: E.23 Chain D: D.16 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:D.16, D:D.16, B:E.23, H2O.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sayer, C. et al., Crystal Structure and Substrate Specificity of the Thermophilic Serine:Pyruvate Aminotransferase from Sulfolobus Solfataricus. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-06-27

Peptides

SERINE-PYRUVATE AMINOTRANSFERASE (AGXT): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

SERINE-PYRUVATE AMINOTRANSFERASE (AGXT)

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