SMTL ID : 2r7m.1

Crystal structure of FAICAR synthetase (PurP) from M. jannaschii complexed with AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: V.53, K.56, R.57 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.56, A:R.57 SO4.6: 3 residues within 4Å: Chain B: V.53, K.56, R.57 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.56, B:R.57 SO4.11: 3 residues within 4Å: Chain C: V.53, K.56, R.57 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.56, C:R.57 SO4.16: 3 residues within 4Å: Chain D: V.53, K.56, R.57 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.56, D:R.57 SO4.21: 3 residues within 4Å: Chain E: V.53, K.56, R.57 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:K.56, E:R.57 SO4.26: 3 residues within 4Å: Chain F: V.53, K.56, R.57 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:K.56, F:R.57

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

CL.2: 5 residues within 4Å: Chain A: H.27, R.314, D.316, G.317 Ligands: AMP.5 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain A: H.210, F.294, V.315, D.316, T.319, M.339 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: H.27, R.314, D.316, G.317 Ligands: AMP.10 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: H.210, F.294, V.315, D.316, T.319, M.339 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain C: H.27, R.314, D.316, G.317 Ligands: AMP.15 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain C: H.210, F.294, V.315, D.316, T.319, M.339 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain D: H.27, R.314, D.316, G.317 Ligands: AMP.20 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain D: H.210, F.294, V.315, D.316, T.319, M.339 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain E: H.27, R.314, D.316, G.317 Ligands: AMP.25 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain E: H.210, F.294, V.315, D.316, T.319, M.339 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain F: H.27, R.314, D.316, G.317 Ligands: AMP.30 Ligand excluded by PLIP CL.28: 6 residues within 4Å: Chain F: H.210, F.294, V.315, D.316, T.319, M.339 Ligand excluded by PLIP

12 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 15 residues within 4Å: Chain A: P.140, I.154, K.156, Y.166, E.199, E.200, Y.201, V.202, R.228, E.230, Y.253, L.299, F.309, E.310 Chain B: R.238 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.156, A:E.199, A:V.202, A:E.310, A:E.310, B:R.238, B:R.238 Water bridges: A:N.206, A:Q.297 Salt bridges: A:K.156 AMP.5: 11 residues within 4Å: Chain A: S.26, H.27, S.94, R.228, I.255, N.258, G.317, G.318 Chain C: R.264, S.266 Ligands: CL.2 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:S.26, A:N.258, A:N.258, C:R.264, C:S.266, C:S.266 Water bridges: A:S.94, A:N.320, A:N.320, C:E.265, C:S.266 pi-Cation interactions: A:H.27 Salt bridges: C:R.264 AMP.9: 15 residues within 4Å: Chain B: P.140, I.154, K.156, Y.166, E.199, E.200, Y.201, V.202, R.228, E.230, Y.253, L.299, F.309, E.310 Chain C: R.238 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.156, B:E.199, B:V.202, B:E.310, B:E.310, C:R.238, C:R.238 Water bridges: B:N.206, B:Q.297 Salt bridges: B:K.156 AMP.10: 11 residues within 4Å: Chain A: R.264, S.266 Chain B: S.26, H.27, S.94, R.228, I.255, N.258, G.317, G.318 Ligands: CL.7 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.26, B:N.258, B:N.258, A:R.264, A:S.266, A:S.266 Water bridges: B:S.94, B:N.320, B:N.320, A:E.265, A:S.266 pi-Cation interactions: B:H.27 Salt bridges: A:R.264 AMP.14: 15 residues within 4Å: Chain A: R.238 Chain C: P.140, I.154, K.156, Y.166, E.199, E.200, Y.201, V.202, R.228, E.230, Y.253, L.299, F.309, E.310 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:K.156, C:E.199, C:V.202, C:E.310, C:E.310, A:R.238, A:R.238 Water bridges: C:N.206, C:Q.297 Salt bridges: C:K.156 AMP.15: 11 residues within 4Å: Chain B: R.264, S.266 Chain C: S.26, H.27, S.94, R.228, I.255, N.258, G.317, G.318 Ligands: CL.12 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:S.26, C:N.258, C:N.258, B:R.264, B:S.266, B:S.266 Water bridges: C:S.94, C:N.320, C:N.320, B:E.265, B:S.266 pi-Cation interactions: C:H.27 Salt bridges: B:R.264 AMP.19: 15 residues within 4Å: Chain D: P.140, I.154, K.156, Y.166, E.199, E.200, Y.201, V.202, R.228, E.230, Y.253, L.299, F.309, E.310 Chain E: R.238 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:K.156, D:Y.166, D:E.199, D:E.199, D:V.202, D:E.310, E:R.238, E:R.238 Water bridges: D:N.206, D:Q.297 Salt bridges: D:K.156 AMP.20: 11 residues within 4Å: Chain D: S.26, H.27, S.94, R.228, I.255, N.258, G.317, G.318 Chain F: R.264, S.266 Ligands: CL.17 12 PLIP interactions: 5 interactions with chain F, 7 interactions with chain D Hydrogen bonds: F:S.266, F:S.266, D:S.26, D:N.258, D:N.258 Water bridges: F:E.265, F:S.266, D:S.94, D:N.320, D:N.320 Salt bridges: F:R.264 pi-Cation interactions: D:H.27 AMP.24: 15 residues within 4Å: Chain E: P.140, I.154, K.156, Y.166, E.199, E.200, Y.201, V.202, R.228, E.230, Y.253, L.299, F.309, E.310 Chain F: R.238 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:K.156, E:Y.166, E:E.199, E:E.199, E:V.202, E:E.310, F:R.238, F:R.238 Water bridges: E:N.206, E:Q.297 Salt bridges: E:K.156 AMP.25: 11 residues within 4Å: Chain D: R.264, S.266 Chain E: S.26, H.27, S.94, R.228, I.255, N.258, G.317, G.318 Ligands: CL.22 12 PLIP interactions: 5 interactions with chain D, 7 interactions with chain E Hydrogen bonds: D:S.266, D:S.266, E:S.26, E:N.258, E:N.258 Water bridges: D:E.265, D:S.266, E:S.94, E:N.320, E:N.320 Salt bridges: D:R.264 pi-Cation interactions: E:H.27 AMP.29: 15 residues within 4Å: Chain D: R.238 Chain F: P.140, I.154, K.156, Y.166, E.199, E.200, Y.201, V.202, R.228, E.230, Y.253, L.299, F.309, E.310 11 PLIP interactions: 2 interactions with chain D, 9 interactions with chain F Hydrogen bonds: D:R.238, D:R.238, F:K.156, F:Y.166, F:E.199, F:E.199, F:V.202, F:E.310 Water bridges: F:N.206, F:Q.297 Salt bridges: F:K.156 AMP.30: 11 residues within 4Å: Chain E: R.264, S.266 Chain F: S.26, H.27, S.94, R.228, I.255, N.258, G.317, G.318 Ligands: CL.27 12 PLIP interactions: 7 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:S.26, F:N.258, F:N.258, E:S.266, E:S.266 Water bridges: F:S.94, F:N.320, F:N.320, E:E.265, E:S.266 pi-Cation interactions: F:H.27 Salt bridges: E:R.264

Links

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Citation

Zhang, Y. et al., Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii. Biochemistry (2008)

Release Date

2007-12-04

Peptides

5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase

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