SMTL ID : 6hwr.1 (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

hetero-1-1-mer

Ligands

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.1: 4 residues within 4Å: Chain A: K.389, N.390, H.393, W.413 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.2: 7 residues within 4Å: Chain B: K.389, N.390, R.391, T.392, H.393, W.413 Ligands: SO4.34 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.413

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, H1T.19 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.158, A:H.280, A:H.317 ZN.20: 7 residues within 4Å: Chain B: D.129, D.158, N.195, H.280, H.317 Ligands: FE.21, H1W.46 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, H1T.19 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.129, A:D.158, A:Y.161, A:H.319 FE.21: 6 residues within 4Å: Chain B: D.129, D.158, Y.161, H.319 Ligands: ZN.20, H1W.46 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: S.55, N.58, R.62, K.90, Y.95 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: 4 residues within 4Å: Chain A: M.366, Q.368, Q.370, R.377 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: R.34, K.90, Y.91 Ligand excluded by PLIP SO4.9: 1 residues within 4Å: Chain A: R.106 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: K.148, K.389, H.395, W.413 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: R.34, Y.91, Q.115 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain B: K.1, R.3 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain B: N.288, H.289, N.365 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain B: G.404, V.405 Ligand excluded by PLIP SO4.25: 1 residues within 4Å: Chain B: Q.368 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain A: E.293 Chain B: R.252, Y.257, K.300 Ligands: NA.18 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: K.268, R.269, S.270 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain B: K.90, Y.91 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain B: R.34, Y.91, Q.115 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain B: K.148, K.389, H.395 Ligands: SO4.34 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain B: V.342, K.343 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain B: M.366, Q.368, R.377 Ligand excluded by PLIP SO4.33: 1 residues within 4Å: Chain B: R.3 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain B: W.413 Ligands: NAG-FUC-NAG.2, NAG-FUC-NAG.2, SO4.30 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain B: P.16, G.17 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 8 residues within 4Å: Chain A: R.298, T.299, N.329, I.330, A.331, Y.332 Chain B: M.292, E.295 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

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

EDO.13: 4 residues within 4Å: Chain A: R.252, Y.257, K.300 Chain B: E.293 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:E.295 Hydrogen bonds: A:R.252, A:Y.257, A:K.300 EDO.14: 2 residues within 4Å: Chain A: L.118, R.391 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.391, A:R.391 EDO.36: 6 residues within 4Å: Chain B: Y.165, P.166, N.167, H.168, E.203, I.204 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.167 EDO.37: 2 residues within 4Å: Chain B: K.1, R.164 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.1, B:R.164 EDO.38: 2 residues within 4Å: Chain B: V.412, W.413 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.413 Water bridges: B:W.413 EDO.39: 4 residues within 4Å: Chain B: N.2, D.4, R.164, Y.165 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.164, B:R.164 Water bridges: B:N.2, B:D.4, B:R.164 EDO.40: 2 residues within 4Å: Chain B: R.252, K.261 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.252, B:R.252, B:K.261 Water bridges: B:Y.257, B:Y.257

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

PGE.15: 3 residues within 4Å: Chain A: T.70, Y.71, R.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.70, A:T.70, A:R.72 PGE.41: 3 residues within 4Å: Chain B: T.70, Y.71, R.72 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.70, B:T.70, B:R.72 PGE.42: 3 residues within 4Å: Chain B: P.16, R.106, R.107 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.106, B:R.107 Water bridges: B:R.106

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

NAG.16: 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:S.141 Water bridges: A:D.10, A:S.141 NAG.17: 2 residues within 4Å: Chain A: N.75, N.167 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.167 NAG.43: 6 residues within 4Å: Chain B: M.5, 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:S.141 Water bridges: B:D.10 NAG.44: 2 residues within 4Å: Chain B: N.75, N.167 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.167

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

NA.18: 4 residues within 4Å: Chain A: E.293 Chain B: R.252 Ligands: H1T.19, SO4.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.252 NA.45: 5 residues within 4Å: Chain A: Y.247, E.293 Chain B: G.251, R.252, K.300 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.252, B:K.300, A:E.293 Water bridges: A:E.293, A:A.296

1 x H1T: [[[[bis($l^{1}-oxidanyl)-[$l^{1}-oxidanyl-[tris($l^{1}-oxidanyl)vanadiooxy]vanadio]oxy-vanadio]oxy-bis($l^{1}-oxidanyl)vanadio]oxy-oxidanylidene-vanadio]-[bis($l^{1}-oxidanyl)vanadio]-$l^{3}-oxidanyl]-tetrakis($l^{1}-oxidanyl)vanadium(Non-covalent)

H1T.19: 18 residues within 4Å: Chain A: D.129, D.158, Y.161, N.195, H.196, H.280, N.288, H.289, H.290, F.291, E.293, H.317, H.319, Y.359 Chain B: R.252 Ligands: ZN.3, FE.4, NA.18 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.195, A:H.289, A:H.289, A:H.290, A:F.291, A:H.317, A:Y.359, B:R.252 Water bridges: A:N.195, A:N.288, A:N.288, A:N.288, A:N.288, A:H.289, A:H.290, A:Y.359, B:R.252

1 x H1W: pentakis(oxidanyl)vanadium(Non-covalent)

H1W.46: 12 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 Ligands: ZN.20, FE.21 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.129, B:D.129, B:D.129, B:N.195, B:N.195, B:H.317, B:H.317

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

IPA.47: 7 residues within 4Å: Chain B: S.146, K.148, H.383, M.385, S.397, N.399, E.408 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:M.385, B:N.399 Hydrogen bonds: B:S.146, B:S.146, B:S.397

1 x VN3: VANADATE ION(Non-covalent)

VN3.48: 2 residues within 4Å: Chain B: K.61, R.107 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.61, B:R.107, B:R.107

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

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

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

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