SMTL ID : 1o7j.1

Atomic resolution structure of Erwinia chrysanthemi L-asparaginase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 9 residues within 4Å: Chain A: G.14, T.15, Y.29, A.31, A.61, S.62, G.94, T.95, D.96 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.15, A:T.15, A:S.62, A:S.62, A:S.62, A:T.95, A:T.95, A:D.96 Water bridges: A:T.15, A:I.16, A:T.95, C:S.254 SO4.2: 5 residues within 4Å: Chain A: K.30, N.59, M.60, A.61, N.64 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.59, A:A.61, A:N.64 Salt bridges: A:K.30 SO4.9: 9 residues within 4Å: Chain B: G.14, T.15, Y.29, A.31, A.61, S.62, G.94, T.95, D.96 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:T.15, B:S.62, B:S.62, B:S.62, B:T.95, B:T.95, B:D.96 Water bridges: B:T.15, B:I.16, B:T.95, D:S.254 SO4.10: 5 residues within 4Å: Chain B: L.267, L.290, P.291, G.292, L.293 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.292 SO4.14: 9 residues within 4Å: Chain C: G.14, T.15, Y.29, A.31, A.61, S.62, G.94, T.95, D.96 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.15, C:T.15, C:S.62, C:S.62, C:S.62, C:T.95, C:T.95, C:D.96 Water bridges: C:I.16, C:Y.29, C:Y.29, A:S.254 SO4.15: 4 residues within 4Å: Chain C: N.59, M.60, A.61, N.64 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.61, C:N.64 SO4.16: 9 residues within 4Å: Chain D: G.14, T.15, Y.29, A.31, A.61, S.62, G.94, T.95, D.96 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:T.15, D:T.15, D:S.62, D:S.62, D:S.62, D:T.95, D:T.95, D:D.96 Water bridges: D:I.16, D:Y.29, D:Y.29, B:S.254 SO4.17: 4 residues within 4Å: Chain D: N.59, M.60, A.61, N.64 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.61, D:A.61, D:N.64

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: G.67, D.68, S.216, L.217, K.219, R.304, M.308 Chain C: D.228 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:D.68, A:L.217 Water bridges: A:G.67, A:K.219, A:V.220, C:D.228, C:D.228, C:D.228 GOL.18: 7 residues within 4Å: Chain A: N.180, E.181 Chain C: R.178 Chain D: R.159, R.178, N.180, Y.184 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:R.178, C:R.178, D:R.159, D:N.180, D:Y.184 Water bridges: D:R.178, D:R.178, D:R.178, D:N.180

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

EDO.4: 3 residues within 4Å: Chain A: K.243 Ligands: EDO.5, EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.243 EDO.5: 3 residues within 4Å: Chain A: K.243 Ligands: EDO.4, EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.243 EDO.6: 5 residues within 4Å: Chain A: G.241, K.243 Ligands: EDO.5, EDO.7, EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.243 Hydrogen bonds: A:K.243 EDO.7: 6 residues within 4Å: Chain A: V.242, K.243, K.269, G.270 Ligands: EDO.6, EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.243 Hydrogen bonds: A:K.243 EDO.8: 5 residues within 4Å: Chain A: K.243, G.270 Ligands: EDO.4, EDO.6, EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.243 EDO.11: 3 residues within 4Å: Chain B: R.212, G.213 Ligands: EDO.12 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain B: E.79, R.212 Ligands: EDO.11, EDO.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.212 EDO.13: 6 residues within 4Å: Chain B: N.78, E.79, A.82, K.110, R.212 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.212 Water bridges: B:K.110 EDO.19: 5 residues within 4Å: Chain D: V.69, K.72 Ligands: EDO.20, EDO.21, EDO.22 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.69, D:K.72 Hydrogen bonds: D:K.72 EDO.20: 6 residues within 4Å: Chain D: F.57, S.58, V.69, K.72 Ligands: EDO.19, EDO.21 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.72 EDO.21: 4 residues within 4Å: Chain D: K.72 Ligands: EDO.19, EDO.20, EDO.22 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.72 EDO.22: 3 residues within 4Å: Chain D: K.72 Ligands: EDO.19, EDO.21 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lubkowski, J. et al., Atomic Resolution Structure of Erwinia Chrysanthemi L-Asparaginase. Acta Crystallogr.,Sect.D (2003)

Release Date

2002-12-04

Peptides

L-ASPARAGINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-ASPARAGINASE

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