SMTL ID : 6py9.1

Crystal structure of red kidney bean purple acid phosphatase in complex with adenosine diphosphate metavanadate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 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.1: 4 residues within 4Å: Chain A: K.422, N.423, H.426, W.446 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.446 NAG-FUC-NAG.2: 5 residues within 4Å: Chain B: K.422, N.423, H.426, W.446 Ligands: EDO.41 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.446 NAG-FUC-NAG.3: 6 residues within 4Å: Chain C: K.422, N.423, R.424, T.425, H.426, W.446 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.426 Hydrophobic interactions: C:W.446 NAG-FUC-NAG.4: 7 residues within 4Å: Chain D: K.422, N.423, R.424, T.425, H.426, W.446, Y.453 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.446

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 7 residues within 4Å: Chain A: D.162, D.191, N.228, H.313, H.350 Ligands: FE.6, AD9.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.191, A:H.313, A:H.350, H2O.1 ZN.32: 7 residues within 4Å: Chain B: D.162, D.191, N.228, H.313, H.350 Ligands: FE.33, P4J.37 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.191, B:H.313, B:H.350 ZN.54: 6 residues within 4Å: Chain C: D.162, D.191, N.228, H.313, H.350 Ligands: FE.55 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.191, C:H.313, C:H.350 ZN.70: 7 residues within 4Å: Chain D: D.162, D.191, N.228, H.313, H.350 Ligands: FE.71, AD9.74 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.191, D:H.313, D:H.350, H2O.38

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

FE.6: 7 residues within 4Å: Chain A: D.162, D.191, Y.194, H.350, H.352 Ligands: ZN.5, AD9.10 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.162, A:D.191, A:Y.194, A:H.352, H2O.1 FE.33: 6 residues within 4Å: Chain B: D.162, D.191, Y.194, H.352 Ligands: ZN.32, P4J.37 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.162, B:D.191, B:Y.194, B:H.352 FE.55: 6 residues within 4Å: Chain C: D.162, D.191, Y.194, H.350, H.352 Ligands: ZN.54 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.162, C:D.191, C:Y.194, C:H.352 FE.71: 6 residues within 4Å: Chain D: D.162, D.191, Y.194, H.352 Ligands: ZN.70, AD9.74 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.162, D:D.191, D:Y.194, D:H.352, H2O.38

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

NAG.7: 7 residues within 4Å: Chain A: M.38, S.42, D.43, V.44, F.167, N.170, S.174 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.167 Hydrogen bonds: A:D.43, A:D.43, A:N.170, A:S.174, A:R.215 NAG.8: 3 residues within 4Å: Chain A: N.108 Chain D: Y.51, D.77 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.200 NAG.9: 3 residues within 4Å: Chain A: Y.51, R.135, N.136 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.135 NAG.34: 3 residues within 4Å: Chain B: Y.51, R.135, N.136 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.51 Hydrogen bonds: B:N.136 Water bridges: B:Y.51, B:R.135 NAG.35: 4 residues within 4Å: Chain B: N.108, N.200 Chain C: Y.51, D.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.200 NAG.36: 8 residues within 4Å: Chain B: M.38, S.42, D.43, V.44, F.167, N.170, S.174, R.215 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.167 Hydrogen bonds: B:D.43, B:D.43, B:N.170, B:S.174 NAG.56: 7 residues within 4Å: Chain C: M.38, S.42, D.43, V.44, F.167, N.170, S.174 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.167 Hydrogen bonds: C:D.43, C:D.43, C:N.170, C:S.174 NAG.57: 3 residues within 4Å: Chain C: Y.51, R.135, N.136 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.51 Hydrogen bonds: C:N.136 Water bridges: C:E.78, C:R.135 NAG.58: 4 residues within 4Å: Chain B: Y.51, D.77 Chain C: N.108, N.200 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:N.108, C:N.200, B:Y.51 Water bridges: C:N.108, B:Y.51, B:E.78 NAG.72: 3 residues within 4Å: Chain A: Y.51, D.77 Chain D: N.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.51 NAG.73: 7 residues within 4Å: Chain D: M.38, S.42, D.43, V.44, F.167, N.170, S.174 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.167 Hydrogen bonds: D:D.43, D:D.43, D:N.170, D:S.174

2 x AD9: ADP METAVANADATE

AD9.10: 15 residues within 4Å: Chain A: D.191, Y.194, N.228, H.229, H.322, H.323, H.350, H.352, Y.392 Chain C: R.285 Ligands: ZN.5, FE.6, GOL.27, GOL.29, PGE.31 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.228, C:R.285 Salt bridges: A:H.229, A:H.322, A:H.323, A:H.323, A:H.352 AD9.74: 15 residues within 4Å: Chain B: R.285 Chain D: Y.194, N.228, H.229, H.322, H.323, H.350, H.352, Y.392 Ligands: EDO.46, GOL.49, ZN.70, FE.71, EDO.82, EDO.87 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:N.228 Water bridges: D:R.197, D:H.323, D:Y.392, D:Y.392, D:Y.392, B:R.285, B:R.285 Salt bridges: D:H.322, D:H.322, D:H.323, D:H.323, B:R.285, B:R.285

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

SO4.11: 5 residues within 4Å: Chain A: S.88, N.91, R.95, K.123, Y.128 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.88, A:N.91, A:Y.128 Water bridges: A:S.88, A:S.88 Salt bridges: A:R.95 SO4.12: 3 residues within 4Å: Chain A: R.67, Y.124, Q.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.148 Salt bridges: A:R.67 SO4.13: 4 residues within 4Å: Chain A: M.399, Q.401, Q.403, R.410 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.401, A:Q.403 Water bridges: A:Q.403, A:R.410 Salt bridges: A:R.410 SO4.38: 3 residues within 4Å: Chain B: R.67, K.123, Y.124 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.124 Water bridges: B:R.67, B:R.67 Salt bridges: B:R.67 SO4.39: 4 residues within 4Å: Chain B: M.399, Q.401, Q.403, R.410 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.401, B:R.410 Water bridges: B:Q.403, B:R.410 Salt bridges: B:R.410 SO4.59: 4 residues within 4Å: Chain A: E.326 Chain C: R.285, Y.290, K.333 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.290 Water bridges: C:Y.290, C:Y.290, C:K.333 Salt bridges: C:K.333 SO4.60: 4 residues within 4Å: Chain C: M.399, Q.401, Q.403, R.410 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.401, C:Q.403 Water bridges: C:Q.403, C:R.410 Salt bridges: C:R.410 SO4.61: 3 residues within 4Å: Chain C: R.67, Y.124, Q.148 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.124, C:Y.124, C:Q.148 Water bridges: C:R.67, C:R.67 Salt bridges: C:R.67 SO4.62: 4 residues within 4Å: Chain C: S.397, N.398, M.399, Q.401 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:M.399, C:M.399, C:Q.401 SO4.63: 3 residues within 4Å: Chain C: R.67, K.123, Y.124 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.124, C:Y.124 Salt bridges: C:R.67 SO4.75: 4 residues within 4Å: Chain D: S.397, N.398, M.399, Q.401 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.397, D:M.399, D:Q.401

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

NA.14: 5 residues within 4Å: Chain A: G.284, R.285, K.333 Chain C: Y.280, E.326 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Water bridges: C:Y.280, C:S.314 Hydrogen bonds: A:R.285, A:K.333 NA.40: 1 residues within 4Å: Ligands: P4J.37 No protein-ligand interaction detected (PLIP) NA.64: 5 residues within 4Å: Chain A: Y.280, E.326 Chain C: G.284, R.285, K.333 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.285, C:K.333, C:K.333 Water bridges: A:S.314, A:E.326

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

EDO.15: 3 residues within 4Å: Chain A: K.100, H.116, T.118 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: V.300, K.301, R.302, S.303, H.451 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: R.356, S.444 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: D.436, G.437, V.440 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: R.67, K.123, Y.124 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: Y.290, K.333 Chain C: E.326 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: W.337, K.340, Y.341 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: K.100, M.101 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Chain A: E.236 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain B: K.422, W.446 Ligands: NAG-FUC-NAG.2, NAG-FUC-NAG.2 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain B: M.76, S.111, G.112 Chain C: R.105, N.108, S.110 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain B: R.85, L.134, T.138 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain B: Y.198, P.199, N.200, H.201, A.234, E.236, I.237 Ligand excluded by PLIP EDO.45: 1 residues within 4Å: Chain B: S.397 Ligand excluded by PLIP EDO.46: 2 residues within 4Å: Ligands: GOL.51, AD9.74 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain B: G.393, V.394, I.395 Ligand excluded by PLIP EDO.65: 3 residues within 4Å: Chain C: D.63, L.64, A.256 Ligand excluded by PLIP EDO.66: 3 residues within 4Å: Chain C: D.396, S.397, N.398 Ligand excluded by PLIP EDO.67: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain C: Q.258, W.292, K.295, K.299 Ligand excluded by PLIP EDO.76: 3 residues within 4Å: Chain D: D.63, L.64, A.256 Ligand excluded by PLIP EDO.77: 3 residues within 4Å: Chain D: L.40, Y.198, R.205 Ligand excluded by PLIP EDO.78: 3 residues within 4Å: Chain D: R.67, Y.124, Q.148 Ligand excluded by PLIP EDO.79: 4 residues within 4Å: Chain B: E.326 Chain D: R.285, Y.290, K.333 Ligand excluded by PLIP EDO.80: 2 residues within 4Å: Chain D: Q.258, K.295 Ligand excluded by PLIP EDO.81: 7 residues within 4Å: Chain A: R.105, N.108, S.110 Chain D: M.76, S.111, G.112, F.113 Ligand excluded by PLIP EDO.82: 1 residues within 4Å: Ligands: AD9.74 Ligand excluded by PLIP EDO.83: 1 residues within 4Å: Chain D: R.433 Ligand excluded by PLIP EDO.84: 4 residues within 4Å: Chain D: D.436, G.437, V.440 Ligands: EDO.85 Ligand excluded by PLIP EDO.85: 3 residues within 4Å: Chain D: G.437, V.438 Ligands: EDO.84 Ligand excluded by PLIP EDO.86: 2 residues within 4Å: Chain D: V.440, E.441 Ligand excluded by PLIP EDO.87: 1 residues within 4Å: Ligands: AD9.74 Ligand excluded by PLIP

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.24: 3 residues within 4Å: Chain A: P.49, R.139, R.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.139, A:R.140 GOL.25: 2 residues within 4Å: Chain A: R.433, Q.435 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.433, A:R.433, A:Q.435 GOL.26: 6 residues within 4Å: Chain A: T.332, N.362, I.363, A.364, Y.365 Chain C: E.328 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.331, A:T.332, A:N.362, A:I.363, A:Y.365 Water bridges: A:R.331, A:R.331 GOL.27: 5 residues within 4Å: Chain A: D.196, N.228, H.229, I.231 Ligands: AD9.10 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.196, A:N.228 Water bridges: A:N.228, A:I.231, A:E.232, C:R.285, C:R.285 GOL.28: 5 residues within 4Å: Chain A: H.322, I.395, D.396, S.397, N.398 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.395, A:S.397, A:N.398, A:N.398 GOL.29: 1 residues within 4Å: Ligands: AD9.10 No protein-ligand interaction detected (PLIP) GOL.48: 3 residues within 4Å: Chain B: P.49, R.139, R.140 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.139, B:R.140, B:R.140 Water bridges: B:R.139 GOL.49: 1 residues within 4Å: Ligands: AD9.74 No protein-ligand interaction detected (PLIP) GOL.50: 7 residues within 4Å: Chain B: T.332, N.362, I.363, A.364, Y.365 Chain D: M.325, E.328 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain B Water bridges: D:M.325, B:R.331, B:T.332 Hydrogen bonds: B:T.332, B:Y.365, B:Y.365 GOL.51: 2 residues within 4Å: Chain B: W.337 Ligands: EDO.46 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.290, B:R.298, B:K.340 GOL.69: 3 residues within 4Å: Chain C: K.294, K.295, R.298 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.295, C:R.298, C:R.298 GOL.88: 1 residues within 4Å: Chain D: K.340 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.340 GOL.89: 4 residues within 4Å: Chain D: R.356, E.358, A.408, V.445 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.356, D:R.356, D:E.358, D:A.408

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

PGE.30: 5 residues within 4Å: Chain A: S.102, H.116, S.247, Y.248, H.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.102, A:H.116 PGE.31: 1 residues within 4Å: Ligands: AD9.10 No protein-ligand interaction detected (PLIP) PGE.52: 1 residues within 4Å: Chain B: K.340 No protein-ligand interaction detected (PLIP) PGE.92: 4 residues within 4Å: Chain D: N.321, H.322, S.397, N.398 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.397, D:N.398, D:N.398

1 x P4J: [(2~{R},3~{R},4~{R},5~{S})-2-(5-azanylimidazol-1-yl)-4-[[bis(oxidanyl)-[tris(oxidanyl)vanadiooxy]vanadio]oxy-bis(oxidanyl)vanadio]oxy-5-[[bis(oxidanyl)-[tris(oxidanyl)vanadiooxy]vanadio]oxymethyl]oxolan-3-yl]oxy-tris(oxidanyl)vanadium(Non-covalent)

P4J.37: 16 residues within 4Å: Chain B: D.162, D.191, Y.194, D.196, R.197, N.228, H.229, H.313, H.322, H.323, H.350, H.352, Y.392 Ligands: ZN.32, FE.33, NA.40 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain B Water bridges: D:R.285, B:D.196, B:R.197, B:E.232 Hydrogen bonds: B:D.196, B:R.197, B:N.228, B:H.229, B:H.229, B:Y.392, B:Y.392

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

CL.53: 5 residues within 4Å: Chain B: G.284, R.285, K.333 Chain D: Y.280, E.326 Ligand excluded by PLIP

2 x FLC: CITRATE ANION(Non-covalent)

FLC.90: 5 residues within 4Å: Chain D: R.46, P.48, P.49, R.139, R.140 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:R.139 Hydrogen bonds: D:R.140 Water bridges: D:R.139 Salt bridges: D:R.46, D:R.139, D:R.139 FLC.91: 6 residues within 4Å: Chain D: M.399, Q.401, Q.403, A.408, F.409, R.410 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.401, D:Q.403, D:R.410, D:R.410 Salt bridges: D:R.410

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
D

D
C

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

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