SMTL ID : 9hnc.1 (7 other biounits)

Crystal structure of potassium-independent L-asparaginase from Phaseolus vulgaris (PvAIII, PvAspG2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: L.58, E.59, I.61, F.64, A.66, K.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.64, A:A.66 NA.7: 5 residues within 4Å: Chain A: V.111, M.112, T.115, P.116, H.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.115 NA.8: 6 residues within 4Å: Chain B: L.58, E.59, I.61, F.64, A.66, K.68 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.66, B:K.68 NA.15: 5 residues within 4Å: Chain B: V.111, M.112, T.115, P.116, H.117 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.115

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

SO4.2: 2 residues within 4Å: Chain A: K.68, H.141 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.68, A:H.141 SO4.3: 1 residues within 4Å: Chain A: K.44 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.44 SO4.4: 4 residues within 4Å: Chain A: G.10, A.11, N.65, T.187 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.11, A:A.11, A:N.65 Water bridges: A:N.65, A:N.65, A:T.187 SO4.10: 5 residues within 4Å: Chain B: G.10, A.11, N.65, T.187, T.237 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.11, B:N.65, B:T.187, B:T.187, B:T.237 Water bridges: B:N.65

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

CL.5: 4 residues within 4Å: Chain A: G.207, R.215, D.218, G.240 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: R.302, E.312 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: R.26 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: G.207, R.215, G.240 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: R.56 Ligand excluded by PLIP

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

EDO.6: 5 residues within 4Å: Chain A: R.22, P.25, R.26, Q.63, E.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.26, A:R.26, A:Q.63 EDO.9: 5 residues within 4Å: Chain B: K.68, I.143, T.144, A.145, E.146 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.68, B:K.68, B:A.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loch, J.I. et al., Unique double-helical packing of protein molecules in the crystal of potassium-independent L-asparaginase from common bean. Acta Crystallogr D Struct Biol (2025)

Release Date

2025-05-14

Peptides

beta-aspartyl-peptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

beta-aspartyl-peptidase

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