SMTL ID : 5dnc.1 (1 other biounit)

Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T19A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-tetramer

Ligands

4 x ASN: ASPARAGINE(Non-covalent)

ASN.1: 12 residues within 4Å: Chain A: G.41, A.42, M.45, D.107, S.108, G.138, T.139, D.140, A.165, Q.166 Chain D: N.295, Y.331 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:A.42, A:D.107, A:S.108, A:T.139, A:D.140, A:D.140, A:A.165, D:N.295 Water bridges: A:L.43, A:Q.166 Hydrophobic interactions: D:Y.331 ASN.7: 12 residues within 4Å: Chain B: G.41, A.42, M.45, D.107, S.108, G.138, T.139, D.140, A.165, Q.166 Chain C: N.295, Y.331 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:A.42, B:D.107, B:S.108, B:T.139, B:D.140, B:D.140, B:A.165, C:N.295 Water bridges: B:L.43 Hydrophobic interactions: C:Y.331 ASN.12: 12 residues within 4Å: Chain B: N.295, Y.331 Chain C: G.41, A.42, M.45, D.107, S.108, G.138, T.139, D.140, A.165, Q.166 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:A.42, C:D.107, C:D.107, C:S.108, C:T.139, C:D.140, C:A.165, B:N.295 Water bridges: C:L.43, C:T.139, B:Y.331 ASN.17: 12 residues within 4Å: Chain A: N.295, Y.331 Chain D: G.41, A.42, M.45, D.107, S.108, G.138, T.139, D.140, A.165, Q.166 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:A.42, D:D.107, D:D.107, D:S.108, D:T.139, D:D.140, D:A.165, A:N.295 Water bridges: D:L.43, A:Y.331

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

EDO.2: 3 residues within 4Å: Chain A: E.154, Y.357, R.378 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: S.226, P.227, A.229, T.230, T.236, A.238 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: N.224, S.320, C.322, L.323, G.325, D.345, M.346 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: N.256, M.257, E.258, G.360 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: S.201, V.231, G.232 Chain B: K.216, F.217, E.218 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain B: G.44, Q.46, G.55, P.56, G.57, L.58, R.170 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain B: E.154, Y.357, L.377, R.378 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain B: P.227, T.230, T.236, A.238 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain B: N.224, S.320, C.322, L.323, G.325, D.345, M.346 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain C: N.224, S.320, Q.321, C.322, L.323, G.325, D.345, M.346 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain C: S.226, P.227, A.229, T.230, T.236, A.238 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: E.154, Y.357, L.377, R.378 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain C: R.243, K.244, K.246 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain D: G.44, G.55, P.56, G.57, L.58, R.170 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain C: S.201, V.231, G.232 Chain D: K.216, F.217, E.218 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain D: E.154, Y.357, L.377, R.378 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain D: N.224, S.320, C.322, L.323, G.325, D.345, M.346 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schalk, A.M. et al., Experimental Data in Support of a Direct Displacement Mechanism for Type I/II l-Asparaginases. J.Biol.Chem. (2016)

Release Date

2016-01-13

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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