SMTL ID : 2xjc.1

Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with guanosine monophosphate and diadenosine tetraphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.1: 15 residues within 4Å: Chain A: N.70, M.71, D.72, F.175, R.220, V.223, D.224, H.227, K.233, T.267, N.268, S.269, K.310 Ligands: GOL.10, MG.11 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:N.70, A:N.70, A:M.71, A:D.72, A:D.72, A:R.220, A:R.220, A:D.224, A:K.233, A:N.268, A:S.269 Water bridges: A:D.72, A:Y.83, A:N.176, A:H.227, A:K.233, A:N.268, A:N.268, A:N.268, A:K.310, A:K.310 Salt bridges: A:D.224, A:K.310 pi-Stacking: A:F.175, A:H.227, A:H.227 5GP.12: 15 residues within 4Å: Chain B: N.70, M.71, D.72, F.175, R.220, V.223, D.224, H.227, K.233, T.267, N.268, S.269, K.310 Ligands: GOL.21, MG.22 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:N.70, B:N.70, B:M.71, B:D.72, B:R.220, B:R.220, B:D.224, B:D.224, B:K.233, B:T.267, B:N.268, B:S.269 Water bridges: B:D.72, B:Y.83, B:N.176, B:H.227, B:K.233, B:N.268, B:N.268, B:N.268, B:K.310, B:K.310 Salt bridges: B:D.224, B:K.310 pi-Stacking: B:F.175, B:H.227, B:H.227

2 x B4P: BIS(ADENOSINE)-5'-TETRAPHOSPHATE(Non-covalent)

B4P.2: 22 residues within 4Å: Chain A: R.162, D.163, I.170, N.172, F.372, L.376, K.380, Q.471, Y.475 Chain B: R.162, D.163, T.165, I.170, N.172, F.372, L.376, K.380, Q.471, Y.475 Ligands: GOL.6, B4P.13, GOL.17 32 PLIP interactions: 18 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:N.172, A:N.172, A:K.377, A:Q.471, A:Y.475, A:Y.475, B:R.162, B:N.172, B:Q.471, B:Q.471 Water bridges: A:R.162, A:R.162, A:R.162, A:I.170, A:K.380, A:K.380, B:R.162, B:D.163, B:K.377, B:Y.475, B:Y.475 Salt bridges: A:R.162, A:K.380, A:K.380, A:K.380, B:R.162, B:K.380, B:K.380, B:K.380 pi-Stacking: A:F.372, A:F.372, B:F.372 B4P.13: 22 residues within 4Å: Chain A: R.162, D.163, T.165, I.170, N.172, F.372, L.376, K.380, Q.471, Y.475 Chain B: R.162, D.163, I.170, N.172, F.372, L.376, K.380, Q.471, Y.475 Ligands: B4P.2, GOL.6, GOL.17 33 PLIP interactions: 19 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:N.172, B:N.172, B:K.377, B:Q.471, B:Y.475, B:Y.475, A:R.162, A:N.172, A:Q.471, A:Q.471, A:Y.475 Water bridges: B:R.162, B:R.162, B:R.162, B:D.163, B:I.170, B:K.380, B:K.380, A:R.162, A:K.377, A:K.380, A:Y.475 Salt bridges: B:R.162, B:K.380, B:K.380, B:K.380, A:R.162, A:K.380, A:K.380, A:K.380 pi-Stacking: B:F.372, B:F.372, A:F.372

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: P.114, T.115, E.392, E.396, Y.452, G.456, L.458 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: R.57, K.379, R.385, D.477 Chain B: D.131, Y.133, N.135 Ligand excluded by PLIP GOL.5: 9 residues within 4Å: Chain A: L.27, T.74, L.75, V.77, V.245, D.247, S.482, F.483, I.484 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: Y.169, I.170, N.172, N.176, H.370 Ligands: B4P.2, B4P.13 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: D.275, T.279, P.296, W.297, Q.298 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: D.270, Y.271, V.306, D.307, G.328, L.330 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain A: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: Y.228, K.233, N.268, S.269 Ligands: 5GP.1 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: P.114, T.115, E.392, E.396, Y.452, G.456, L.458 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain A: D.131, Y.133, N.135 Chain B: R.57, K.379, R.385, D.477 Ligand excluded by PLIP GOL.16: 9 residues within 4Å: Chain B: L.27, T.74, L.75, V.77, V.245, D.247, S.482, F.483, I.484 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain B: Y.169, I.170, N.172, N.176, H.370 Ligands: B4P.2, B4P.13 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: D.275, T.279, P.296, W.297, Q.298 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain B: D.270, Y.271, V.306, D.307, G.328, L.330 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain B: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: Y.228, K.233, N.268, S.269 Ligands: 5GP.12 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 4 residues within 4Å: Chain A: N.70, D.72, D.369 Ligands: 5GP.1 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:D.72, A:D.369, 5GP.1, H2O.12, H2O.12 MG.22: 4 residues within 4Å: Chain B: N.70, D.72, D.369 Ligands: 5GP.12 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:D.72, B:D.369, 5GP.12, H2O.27, H2O.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wallden, K. et al., Structural Basis for the Allosteric Regulation and Substrate Recognition of Human Cytosolic 5'-Nucleotidase II. J.Mol.Biol. (2011)

Release Date

2011-03-16

Peptides

CYTOSOLIC PURINE 5'-NUCLEOTIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CYTOSOLIC PURINE 5'-NUCLEOTIDASE

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