SMTL ID : 6vj7.1

Crystal structure of red kidney bean purple acid phosphatase in complex with adenosine 5'-(beta,gamma imido)triphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.1: 5 residues within 4Å: Chain A: K.389, N.390, H.393, W.413 Ligands: EDO.18 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 3 residues within 4Å: Chain A: Y.18, R.102, N.103 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 6 residues within 4Å: Chain B: N.75, P.166, N.167 Chain D: Y.18, D.44, E.45 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.3: 6 residues within 4Å: Chain B: K.389, N.390, H.393, W.413 Ligands: SO4.33, EDO.37 No protein-ligand interaction detected (PLIP)

2 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.5: 3 residues within 4Å: Chain B: Y.18, R.102, N.103 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.6: 6 residues within 4Å: Chain C: K.389, N.390, R.391, T.392, H.393, W.413 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.413

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.7: 5 residues within 4Å: Chain A: Y.18, D.44 Chain C: N.75, P.166, N.167 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.44, A:D.44 NAG-NAG.8: 6 residues within 4Å: Chain D: K.389, N.390, T.392, H.393, W.413 Ligands: EDO.88 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.9: 7 residues within 4Å: Chain A: D.129, D.158, N.195, H.280, H.317 Ligands: FE.10, ANP.26 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.158, A:H.280 ZN.29: 7 residues within 4Å: Chain B: D.129, D.158, N.195, H.280, H.317, H.319 Ligands: FE.30 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.158, B:H.317 ZN.47: 7 residues within 4Å: Chain C: D.129, D.158, N.195, H.280, H.317 Ligands: FE.48, ANP.69 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.158, C:H.280 ZN.72: 7 residues within 4Å: Chain D: D.129, D.158, N.195, H.280, H.317 Ligands: FE.73, ANP.103 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.158, D:H.280, D:H.317

4 x FE: FE (III) ION(Non-covalent)

FE.10: 6 residues within 4Å: Chain A: D.129, D.158, Y.161, H.319 Ligands: ZN.9, ANP.26 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.129, A:D.158, A:Y.161, A:H.319 FE.30: 6 residues within 4Å: Chain B: D.129, D.158, Y.161, H.196, H.319 Ligands: ZN.29 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.129, B:D.158, B:Y.161, B:H.319 FE.48: 6 residues within 4Å: Chain C: D.129, D.158, Y.161, H.319 Ligands: ZN.47, ANP.69 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.129, C:D.158, C:Y.161, C:H.319 FE.73: 7 residues within 4Å: Chain D: D.129, D.158, Y.161, H.196, H.319 Ligands: ZN.72, ANP.103 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.129, D:D.158, D:Y.161, D:H.319

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

SO4.11: 6 residues within 4Å: Chain A: S.55, N.58, R.60, R.62, K.90, Y.95 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: M.366, Q.368, Q.370, R.377 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: R.106, R.107, F.108, Y.186 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain B: N.288, H.289, N.365 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain B: V.342, K.343 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain B: K.389, W.413 Ligands: NAG-NAG-BMA-BMA.3, NAG-NAG-BMA-BMA.3 Ligand excluded by PLIP SO4.34: 1 residues within 4Å: Chain B: R.3 Ligand excluded by PLIP SO4.45: 9 residues within 4Å: Chain B: G.251, R.252, K.300 Chain C: S.246, Y.247, Y.250, S.281, E.293 Ligands: NA.70 Ligand excluded by PLIP SO4.49: 1 residues within 4Å: Chain C: R.3 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain C: Q.368, Q.370, R.377 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain C: R.34, K.90, Y.91 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain C: R.34, Y.91, Q.115 Ligand excluded by PLIP SO4.53: 4 residues within 4Å: Chain C: N.2, D.4, R.164, Y.165 Ligand excluded by PLIP SO4.54: 4 residues within 4Å: Chain C: K.268, R.269, S.270, H.418 Ligand excluded by PLIP SO4.55: 1 residues within 4Å: Chain C: R.3 Ligand excluded by PLIP SO4.74: 2 residues within 4Å: Chain D: K.1, R.3 Ligand excluded by PLIP SO4.75: 3 residues within 4Å: Chain D: N.288, H.289, N.365 Ligand excluded by PLIP SO4.76: 1 residues within 4Å: Chain D: Q.368 Ligand excluded by PLIP SO4.77: 7 residues within 4Å: Chain A: E.293 Chain D: R.252, Y.257, K.300 Ligands: ANP.26, PG4.71, EDO.91 Ligand excluded by PLIP SO4.78: 4 residues within 4Å: Chain D: K.268, R.269, S.270, H.418 Ligand excluded by PLIP SO4.79: 3 residues within 4Å: Chain D: R.34, K.90, Y.91 Ligand excluded by PLIP SO4.80: 4 residues within 4Å: Chain D: V.32, R.34, Y.91, Q.115 Ligand excluded by PLIP SO4.81: 3 residues within 4Å: Chain D: K.389, H.395 Ligands: EDO.88 Ligand excluded by PLIP SO4.82: 3 residues within 4Å: Chain D: R.52, L.101, T.105 Ligand excluded by PLIP

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 9 residues within 4Å: Chain A: R.298, T.299, N.329, I.330, A.331, Y.332 Chain D: M.292, E.295 Ligands: PGE.100 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.298, A:T.299, A:I.330, A:Y.332 Water bridges: A:R.298 GOL.15: 3 residues within 4Å: Chain A: N.288, H.289, D.363 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.289 GOL.16: 4 residues within 4Å: Chain A: K.67, S.214, Y.215, H.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.69, A:Y.215 Water bridges: A:Y.215, A:Y.215 GOL.17: 2 residues within 4Å: Chain A: K.90, Y.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.90, A:Y.91 GOL.56: 7 residues within 4Å: Chain B: M.292, E.295 Chain C: T.299, N.329, I.330, A.331, Y.332 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.298, C:T.299, C:I.330, C:Y.332 GOL.83: 7 residues within 4Å: Chain A: R.252, G.253 Chain D: D.163, N.195, H.196 Ligands: EDO.94, ANP.103 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.195, D:H.196, A:R.252 GOL.84: 10 residues within 4Å: Chain A: M.292, E.295 Chain D: R.298, T.299, N.329, I.330, A.331, Y.332 Ligands: PG4.27, PGE.100 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.298, D:R.298, D:I.330, D:Y.332 Water bridges: D:T.299, A:M.292 GOL.85: 4 residues within 4Å: Chain D: M.366, Q.368, Q.370, R.377 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.368, D:Q.370, D:R.377 Water bridges: D:R.377 GOL.86: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

31 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.18: 3 residues within 4Å: Chain A: W.413 Ligands: NAG-NAG-BMA-BMA.1, NAG-NAG-BMA-BMA.1 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain A: R.400, Q.402 Ligand excluded by PLIP EDO.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.22: 1 residues within 4Å: Chain A: F.134 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: H.418, W.419, P.421 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain B: T.299, N.329, I.330, Y.332 Chain C: M.292 Ligand excluded by PLIP EDO.37: 1 residues within 4Å: Ligands: NAG-NAG-BMA-BMA.3 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain B: N.2, D.4, R.164, Y.165, P.166 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain B: L.118, S.270 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain B: P.46, G.47, S.49, M.68, H.82 Ligand excluded by PLIP EDO.57: 2 residues within 4Å: Chain C: R.106, F.108 Ligand excluded by PLIP EDO.58: 2 residues within 4Å: Chain C: R.323, E.325 Ligand excluded by PLIP EDO.59: 3 residues within 4Å: Chain C: D.163, H.196 Ligands: ANP.69 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain C: S.380, F.381, Q.402 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain C: K.65, G.66, T.85, R.87 Ligand excluded by PLIP EDO.62: 1 residues within 4Å: Chain C: V.32 Ligand excluded by PLIP EDO.63: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.64: 4 residues within 4Å: Chain C: V.14, Q.22, M.43, R.178 Ligand excluded by PLIP EDO.87: 4 residues within 4Å: Chain D: P.166, N.167, E.203, I.204 Ligand excluded by PLIP EDO.88: 5 residues within 4Å: Chain D: K.389, W.413 Ligands: NAG-NAG.8, NAG-NAG.8, SO4.81 Ligand excluded by PLIP EDO.89: 1 residues within 4Å: Chain D: R.3 Ligand excluded by PLIP EDO.90: 4 residues within 4Å: Chain D: N.288, N.365, M.366, Q.368 Ligand excluded by PLIP EDO.91: 7 residues within 4Å: Chain A: S.246, Y.250, E.293 Chain D: G.251, R.252, K.300 Ligands: SO4.77 Ligand excluded by PLIP EDO.92: 7 residues within 4Å: Chain A: W.231, A.249, P.255 Chain D: P.209, F.210, Y.247 Ligands: EDO.93 Ligand excluded by PLIP EDO.93: 1 residues within 4Å: Ligands: EDO.92 Ligand excluded by PLIP EDO.94: 8 residues within 4Å: Chain A: G.253 Chain D: D.163, N.195, H.196, I.198, E.199, F.200 Ligands: GOL.83 Ligand excluded by PLIP EDO.95: 3 residues within 4Å: Chain D: P.202, E.203, N.205 Ligand excluded by PLIP EDO.96: 2 residues within 4Å: Chain D: E.144, R.182 Ligand excluded by PLIP EDO.97: 6 residues within 4Å: Chain D: S.146, H.383, M.385, S.397, N.399, E.408 Ligand excluded by PLIP EDO.98: 2 residues within 4Å: Chain D: K.61, R.107 Ligand excluded by PLIP

7 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.23: 2 residues within 4Å: Ligands: ANP.26, PG4.71 No protein-ligand interaction detected (PLIP) PGE.41: 4 residues within 4Å: Chain B: V.267, K.268, R.269, S.270 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.269, B:S.270 PGE.42: 1 residues within 4Å: Chain B: N.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.205, B:N.205 PGE.65: 6 residues within 4Å: Chain C: N.288, H.289, I.362, D.363, S.364, N.365 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.364, C:N.365, C:N.365 Water bridges: C:D.363 PGE.66: 6 residues within 4Å: Chain A: T.70, Y.71, R.72 Chain C: T.70, Y.71, R.72 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.70, A:Y.71, A:R.72, C:T.70, C:R.72 PGE.99: 6 residues within 4Å: Chain B: T.70, Y.71, R.72 Chain D: T.70, Y.71, R.72 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:Y.71, B:R.72, D:T.70, D:T.70, D:R.72 Water bridges: B:R.72 PGE.100: 9 residues within 4Å: Chain A: R.298, T.299, Y.332 Chain D: E.295, R.298, N.329, Y.332 Ligands: GOL.14, GOL.84 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:E.295, D:R.298, D:R.298, D:N.329 Water bridges: A:R.298

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.24: 7 residues within 4Å: Chain A: M.5, D.10, V.11, N.137, S.141, E.144, R.182 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.10, A:D.10, A:S.141, A:R.182 Water bridges: A:N.137, A:S.141, A:E.144 NAG.25: 3 residues within 4Å: Chain A: N.75, N.167 Chain C: Y.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.75, A:N.167 NAG.43: 7 residues within 4Å: Chain B: M.5, S.9, D.10, V.11, F.134, N.137, S.141 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.134 Hydrogen bonds: B:D.10, B:D.10, B:N.137, B:S.141 NAG.46: 3 residues within 4Å: Chain C: Y.18, R.102, N.103 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.18 Hydrogen bonds: C:R.102, C:N.103 NAG.67: 8 residues within 4Å: Chain C: M.5, D.10, V.11, F.134, N.137, S.141, E.144, R.182 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.134 Hydrogen bonds: C:D.10, C:D.10, C:S.141, C:E.144 Water bridges: C:N.137 NAG.101: 6 residues within 4Å: Chain D: D.10, V.11, F.134, N.137, S.141, R.182 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.134 Hydrogen bonds: D:D.10, D:D.10, D:N.137, D:S.141, D:R.182 NAG.102: 4 residues within 4Å: Chain B: Y.18, D.44 Chain D: N.75, N.167 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.18, B:E.45, D:N.167

3 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.26: 20 residues within 4Å: Chain A: D.129, D.158, Y.161, N.195, H.196, N.288, H.289, H.290, F.291, E.293, H.317, H.319, Y.359 Chain D: R.252 Ligands: ZN.9, FE.10, PGE.23, PG4.27, PG4.71, SO4.77 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:H.289, A:H.290, A:F.291, A:F.291, A:Y.359, D:R.252 Water bridges: A:N.195, A:H.196, A:Y.359, A:Y.359 Salt bridges: A:H.290 ANP.69: 15 residues within 4Å: Chain B: R.252 Chain C: D.129, D.158, Y.161, N.195, H.196, H.280, H.289, H.290, H.317, H.319, Y.359 Ligands: ZN.47, FE.48, EDO.59 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.161, C:N.195, C:H.290, C:H.319, C:Y.359 Salt bridges: C:H.290, B:R.252 ANP.103: 15 residues within 4Å: Chain A: R.252 Chain D: D.129, D.158, Y.161, N.195, H.196, H.280, H.289, H.290, H.317, H.319, Y.359 Ligands: ZN.72, FE.73, GOL.83 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Y.161, D:N.195, D:H.196, D:H.290, D:H.317 Salt bridges: D:H.289, D:H.290, A:R.252

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.27: 7 residues within 4Å: Chain A: N.288, F.291, M.292 Chain D: K.333 Ligands: ANP.26, PG4.71, GOL.84 1 PLIP interactions: 1 interactions with chain D Water bridges: D:T.299 PG4.71: 8 residues within 4Å: Chain D: R.252, Y.257, K.261, W.304 Ligands: PGE.23, ANP.26, PG4.27, SO4.77 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.252, D:K.261

3 x NA: SODIUM ION(Non-functional Binders)

NA.28: 3 residues within 4Å: Chain A: D.163, H.196, E.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.163, A:E.199 Water bridges: A:Y.161 NA.44: 7 residues within 4Å: Chain B: G.128, D.129, G.354, D.355, A.356, G.357, N.358 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.129, B:A.356, B:G.357, B:N.358 NA.70: 5 residues within 4Å: Chain C: Y.247, S.281, E.293, H.317 Ligands: SO4.45 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.281, C:E.293

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.68: 2 residues within 4Å: Chain C: K.61, R.107 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.107, C:R.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feder, D. et al., Structural elements that modulate the substrate specificity of plant purple acid phosphatases: Avenues for improved phosphorus acquisition in crops. Plant Sci. (2020)

Release Date

2020-04-29

Peptides

Fe(3+)-Zn(2+) purple acid phosphatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Fe(3+)-Zn(2+) purple acid phosphatase

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