SMTL ID : 6hwr.2 (1 other biounit)

Red kidney bean purple acid phosphatase in complex with adenosine divanadate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

1 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: 5 residues within 4Å: Chain A: K.389, N.390, H.393, W.413 Ligands: SO4.11 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 7 residues within 4Å: Chain B: K.389, N.390, R.391, T.392, H.393, W.413 Ligands: SO4.29 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: D.129, D.158, N.195, H.280, H.317 Ligands: FE.4, VV6.20 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.158, A:H.280, A:H.317 ZN.21: 7 residues within 4Å: Chain B: D.129, D.158, N.195, H.280, H.317 Ligands: FE.22, H1Q.45 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.158, B:H.280, B:H.317

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

FE.4: 6 residues within 4Å: Chain A: D.129, D.158, Y.161, H.319 Ligands: ZN.3, VV6.20 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.129, A:D.158, A:Y.161, A:H.319 FE.22: 6 residues within 4Å: Chain B: D.129, D.158, Y.161, H.319 Ligands: ZN.21, H1Q.45 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.129, B:D.158, B:Y.161, B:H.319

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

SO4.5: 5 residues within 4Å: Chain A: R.252, Y.257, T.299, K.300 Chain B: E.293 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: N.288, H.289, D.363, N.365 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: V.342, K.343 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: Q.368, Q.370, R.377 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: R.34, K.90, Y.91 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: V.32, R.34, Y.91, Q.115 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: W.413 Ligands: NAG-FUC-NAG.1, NAG-FUC-NAG.1 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: G.404, V.405 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain B: K.1, R.3 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: M.366, Q.368, Q.370, R.377 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain B: G.404, V.405 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain B: R.52, L.101, T.105 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain B: K.90, Y.91 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain B: R.34, Y.91, Q.115 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain B: W.413 Ligands: NAG-NAG.2, NAG-NAG.2 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain B: V.342, K.343 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain B: N.2, D.4, R.164, Y.165 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain B: K.268, R.269, S.270 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain A: E.293 Chain B: R.252, Y.257, K.300 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain B: L.7, R.172 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain B: N.288, H.289, N.365 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: H.418, W.419, P.421 No protein-ligand interaction detected (PLIP) GOL.14: 3 residues within 4Å: Chain A: K.333 Chain B: N.288 Ligands: GOL.15 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:N.288, A:K.333 GOL.15: 3 residues within 4Å: Chain A: K.333, N.336 Ligands: GOL.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.336 GOL.36: 8 residues within 4Å: Chain A: M.292, E.295 Chain B: R.298, T.299, N.329, I.330, A.331, Y.332 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.298, B:I.330, B:Y.332 Water bridges: B:T.299, B:A.331, A:M.292

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

EDO.16: 5 residues within 4Å: Chain A: P.166, N.167, H.168, E.203, I.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.167 EDO.37: 4 residues within 4Å: Chain B: R.106, R.107, F.108, Y.186 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.106, B:Y.186, B:Y.186 EDO.38: 2 residues within 4Å: Chain B: R.323, D.424 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.323, B:R.323, B:D.424 EDO.39: 3 residues within 4Å: Chain B: K.307, Y.308 Ligands: EDO.40 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.308, B:Y.308 EDO.40: 4 residues within 4Å: Chain B: R.265, K.307, Y.308 Ligands: EDO.39 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.265, B:R.265, B:K.307 Water bridges: B:Y.308

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

NAG.17: 2 residues within 4Å: Chain A: N.75, N.167 No protein-ligand interaction detected (PLIP) NAG.18: 7 residues within 4Å: Chain A: M.5, S.9, D.10, V.11, F.134, N.137, S.141 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.134 Hydrogen bonds: A:D.10, A:D.10, A:N.137, A:S.141 Water bridges: A:S.141 NAG.41: 7 residues within 4Å: Chain B: M.5, D.10, V.11, F.134, N.137, S.141, E.144 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.134 Hydrogen bonds: B:D.10, B:D.10, B:S.141, B:E.144 Water bridges: B:D.10, B:S.141, B:E.144 NAG.42: 2 residues within 4Å: Chain B: N.75, N.167 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.167

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

NA.19: 5 residues within 4Å: Chain A: G.251, R.252, K.300 Chain B: Y.247, E.293 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.293, A:R.252, A:K.300 Water bridges: B:S.281 NA.43: 4 residues within 4Å: Chain A: E.293 Chain B: G.251, R.252, K.300 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.252, B:K.300, B:K.300 Water bridges: A:E.293, A:A.296 NA.44: 3 residues within 4Å: Chain B: N.195, H.290 Ligands: H1Q.45 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.195, B:H.290

1 x VV6: [[[[bis(oxidanyl)-[tris(oxidanyl)vanadiooxy]vanadio]oxy-bis(oxidanyl)vanadio]-oxidanylidene-vanadio]oxy-oxidanyl-vanadio]oxy-tetrakis(oxidanyl)vanadium(Non-covalent)

VV6.20: 15 residues within 4Å: Chain A: D.129, D.158, Y.161, N.195, H.196, H.280, H.289, H.290, E.293, H.317, H.319, Y.359 Chain B: R.252 Ligands: ZN.3, FE.4 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.195, A:H.289, A:H.289, A:H.289, A:H.317, B:R.252, B:R.252, B:R.252 Water bridges: A:H.290, A:E.293, B:R.252

1 x H1Q: adenosine divanadate(Non-covalent)

H1Q.45: 14 residues within 4Å: Chain B: D.129, D.158, Y.161, N.195, H.196, H.280, H.289, H.290, H.317, H.319, Y.359 Ligands: ZN.21, FE.22, NA.44 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.129, B:D.158, B:Y.161, B:Y.161, B:N.195, B:N.195, B:H.317, B:Y.359, B:Y.359, B:Y.359 Water bridges: B:H.289, B:H.319, A:R.252, A:R.252, A:R.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feder, D. et al., The Binding Mode of an ADP Analogue to a Metallohydrolase Mimics the Likely Transition State. Chembiochem (2019)

Release Date

2019-04-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

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

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