SMTL ID : 5dne.1

Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant K188M

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-tetramer

Ligands

4 x ASN: ASPARAGINE(Non-covalent)

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

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

EDO.2: 7 residues within 4Å: Chain A: V.231, G.232, A.233, D.234, V.235 Chain B: V.167, W.173 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.173 EDO.3: 6 residues within 4Å: Chain A: S.201, V.231, G.232 Chain B: K.216, F.217, E.218 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.231, B:F.217, B:E.218 EDO.5: 5 residues within 4Å: Chain A: E.178, S.201 Chain B: N.174, D.175, E.178 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:S.201, B:E.178 Hydrogen bonds: B:N.174 EDO.6: 6 residues within 4Å: Chain B: C.319, S.320, C.322, M.346, T.347, S.348 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.320, B:C.322, B:S.348 Water bridges: B:M.346 EDO.8: 6 residues within 4Å: Chain C: S.226, P.227, A.229, T.230, T.236, A.238 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.226, C:T.236 EDO.9: 6 residues within 4Å: Chain C: K.216, F.217, E.218 Chain D: T.230, V.231, G.232 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.217, C:E.218 EDO.10: 6 residues within 4Å: Chain C: N.224, S.320, C.322, L.323, G.325, M.346 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.224, C:S.320 Water bridges: C:S.320 EDO.11: 6 residues within 4Å: Chain C: S.201, V.231, G.232 Chain D: K.216, F.217, E.218 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:F.217, D:E.218, C:V.231 EDO.13: 7 residues within 4Å: Chain D: N.224, S.320, C.322, L.323, G.325, D.345, M.346 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.224, D:S.320, D:D.345 Water bridges: D:S.348

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