SMTL ID : 4pv2.1

Crystal structure of potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris in complex with K+ and Na+ cations

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

hetero-2-2-mer

Ligands

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

NA.1: 9 residues within 4Å: Chain A: L.60, E.61, D.63, P.64, F.66, S.68, G.69, R.70 Ligands: K.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.68 Water bridges: A:D.63 NA.2: 5 residues within 4Å: Chain A: V.113, M.114, S.117, H.119 Ligands: K.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.113, A:S.117 NA.11: 9 residues within 4Å: Chain C: L.60, E.61, D.63, P.64, F.66, S.68, G.69, R.70 Ligands: K.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.61 Water bridges: C:F.66 NA.12: 5 residues within 4Å: Chain C: V.113, M.114, S.117, H.119 Ligands: K.14 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.117, C:S.117 Water bridges: C:C.94

4 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: L.60, E.61, D.63, F.66, S.68, R.70 Ligands: NA.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:L.60, A:D.63, A:F.66, A:S.68, A:S.68 K.4: 7 residues within 4Å: Chain A: C.94, V.113, M.114, S.117, H.119, S.120 Ligands: NA.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:V.113, A:H.119, H2O.5, H2O.5, H2O.5 K.13: 7 residues within 4Å: Chain C: L.60, E.61, D.63, F.66, S.68, R.70 Ligands: NA.11 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:L.60, C:D.63, C:F.66, C:S.68, H2O.7 K.14: 4 residues within 4Å: Chain C: M.114, S.117, H.119 Ligands: NA.12 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.117, H2O.13, H2O.13

21 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 6 residues within 4Å: Chain A: P.90, K.91, R.92 Chain D: R.59, D.90 Ligands: NO3.8 Ligand excluded by PLIP NO3.6: 3 residues within 4Å: Chain A: E.142, V.145 Ligands: NO3.7 Ligand excluded by PLIP NO3.7: 6 residues within 4Å: Chain A: R.70, E.142, Y.143, V.145, T.146 Ligands: NO3.6 Ligand excluded by PLIP NO3.8: 5 residues within 4Å: Chain A: R.92 Chain B: C.43, D.44, E.71 Ligands: NO3.5 Ligand excluded by PLIP NO3.9: 9 residues within 4Å: Chain B: M.26, R.29 Chain C: K.116, S.117, P.118, I.122, F.130, Q.133 Ligands: NO3.20 Ligand excluded by PLIP NO3.10: 5 residues within 4Å: Chain A: K.29 Chain B: V.127, A.128, I.129, W.130 Ligand excluded by PLIP NO3.15: 5 residues within 4Å: Chain C: G.15, V.16, L.20, R.24 Chain D: F.115 Ligand excluded by PLIP NO3.16: 4 residues within 4Å: Chain A: F.124, S.125 Chain C: F.124, S.125 Ligand excluded by PLIP NO3.17: 2 residues within 4Å: Chain C: R.34, N.37 Ligand excluded by PLIP NO3.18: 2 residues within 4Å: Chain C: R.58, E.137 Ligand excluded by PLIP NO3.19: 3 residues within 4Å: Chain C: E.142, Y.143 Ligands: NO3.21 Ligand excluded by PLIP NO3.20: 6 residues within 4Å: Chain B: R.29 Chain C: G.126, D.129, F.130, Q.133 Ligands: NO3.9 Ligand excluded by PLIP NO3.21: 3 residues within 4Å: Chain C: V.139, D.140 Ligands: NO3.19 Ligand excluded by PLIP NO3.22: 6 residues within 4Å: Chain D: M.70, K.76, L.77, S.100, T.102, E.104 Ligand excluded by PLIP NO3.23: 4 residues within 4Å: Chain C: K.29 Chain D: A.128, I.129, W.130 Ligand excluded by PLIP NO3.24: 3 residues within 4Å: Chain C: R.92 Chain D: C.43, D.44 Ligand excluded by PLIP NO3.25: 4 residues within 4Å: Chain D: H.78, A.106, C.107 Ligands: NO3.28 Ligand excluded by PLIP NO3.26: 7 residues within 4Å: Chain A: S.117, P.118, I.122, F.130, Q.133 Chain D: M.26, R.29 Ligand excluded by PLIP NO3.27: 3 residues within 4Å: Chain D: K.73, L.75, F.83 Ligand excluded by PLIP NO3.28: 7 residues within 4Å: Chain D: A.106, C.107, R.116, C.118, F.124, E.126 Ligands: NO3.25 Ligand excluded by PLIP NO3.29: 4 residues within 4Å: Chain B: E.71, Y.72 Chain D: K.73, F.83 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bejger, M. et al., Na+/K+ exchange switches the catalytic apparatus of potassium-dependent plant L-asparaginase. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-09-03

Peptides

L-ASPARAGINASE ALPHA SUBUNIT: AC
L-ASPARAGINASE BETA SUBUNIT: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

L-ASPARAGINASE ALPHA SUBUNIT

L-ASPARAGINASE BETA SUBUNIT

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