SMTL ID : 4pvq.1

Crystal structure of sulfate-bound human l-asparaginase protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: A.14, G.15, P.16, L.264, S.282, T.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.283, A:T.283 SO4.2: 8 residues within 4Å: Chain A: T.170, T.188, G.190, I.191, R.198, G.222, H.223, G.224 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.170, A:T.188, A:G.190, A:G.224 Water bridges: A:D.201, A:G.222 Salt bridges: A:R.198 SO4.3: 5 residues within 4Å: Chain A: D.214, I.215, I.240, E.241, K.272 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.272 SO4.4: 3 residues within 4Å: Chain A: M.195 Chain B: F.127, A.130 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.126, B:F.127 SO4.5: 4 residues within 4Å: Chain A: Q.126, F.127, A.130 Chain B: M.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.127 Water bridges: A:A.130 SO4.6: 6 residues within 4Å: Chain A: G.75, E.76, V.77, G.138, E.139, V.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.77, A:G.138 SO4.7: 5 residues within 4Å: Chain A: T.34, Y.37, R.41, L.309, P.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.310 Salt bridges: A:R.41 SO4.12: 8 residues within 4Å: Chain B: T.170, T.188, G.190, R.198, G.200, D.201, G.222, G.224 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.170, B:T.170, B:G.224 Water bridges: B:T.170, B:G.222 Salt bridges: B:R.198 SO4.13: 5 residues within 4Å: Chain B: T.34, Y.37, G.38, R.41, L.309 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.38 Salt bridges: B:R.41 SO4.14: 5 residues within 4Å: Chain B: D.214, I.215, I.240, E.241, K.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.241 Salt bridges: B:K.272 SO4.15: 5 residues within 4Å: Chain B: H.2, M.3, C.178, K.179, G.180 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.2, B:M.3, B:K.179 Water bridges: B:H.2, B:H.2, B:H.2 Salt bridges: B:H.2 SO4.16: 3 residues within 4Å: Chain B: Y.256, S.259, R.260 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.259 SO4.17: 6 residues within 4Å: Chain B: E.76, V.77, Q.98, C.99, G.138, L.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.77, B:C.99 Water bridges: B:E.76, B:E.76

4 x IOD: IODIDE ION(Non-functional Binders)

IOD.8: 4 residues within 4Å: Chain A: G.12, L.168, P.286 Ligands: IOD.10 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: E.225, K.229 Chain B: P.115 Ligands: IOD.18 Ligand excluded by PLIP IOD.10: 6 residues within 4Å: Chain A: G.12, F.63, N.64, L.168, G.169 Ligands: IOD.8 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain A: K.229 Chain B: S.90, A.91 Ligands: IOD.9 Ligand excluded by PLIP

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

NA.11: 6 residues within 4Å: Chain A: L.57, E.58, D.60, F.63, A.65, C.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.63, A:A.65, A:A.65 NA.19: 6 residues within 4Å: Chain B: L.57, E.58, D.60, F.63, A.65, C.67 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.60, B:F.63, B:A.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomme, J. et al., Structures of apo and product-bound human L-asparaginase: insights into the mechanism of autoproteolysis and substrate hydrolysis. Biochemistry (2012)

Release Date

2014-03-26

Peptides

Isoaspartyl peptidase/L-asparaginase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoaspartyl peptidase/L-asparaginase

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