SMTL ID : 5dnc.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-octamer

Ligands

8 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 B: N.295, Y.331 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.42, A:D.107, A:S.108, A:T.139, A:D.140, A:D.140, A:A.165, B:N.295 Water bridges: A:L.43 Hydrophobic interactions: B:Y.331 ASN.6: 12 residues within 4Å: Chain A: N.295, Y.331 Chain B: G.41, A.42, M.45, D.107, S.108, G.138, T.139, D.140, A.165, Q.166 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:N.295, B:A.42, B:D.107, B:D.107, B:S.108, B:T.139, B:D.140, B:A.165 Water bridges: A:Y.331, B:L.43, B:T.139 ASN.11: 12 residues within 4Å: Chain C: 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: 8 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:A.42, C:D.107, C:S.108, C:T.139, C:D.140, C:D.140, C:A.165, D:N.295 Water bridges: C:L.43, D:Y.331 Hydrophobic interactions: D:Y.331 ASN.16: 12 residues within 4Å: Chain C: 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: 9 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:A.42, D:D.107, D:D.107, D:S.108, D:T.139, D:D.140, D:A.165, C:N.295 Water bridges: D:L.43, D:K.211 ASN.21: 12 residues within 4Å: Chain E: G.41, A.42, M.45, D.107, S.108, G.138, T.139, D.140, A.165, Q.166 Chain F: N.295, Y.331 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:A.42, E:D.107, E:S.108, E:T.139, E:D.140, E:D.140, E:A.165, F:N.295 Water bridges: E:L.43, E:Q.166 Hydrophobic interactions: F:Y.331 ASN.27: 12 residues within 4Å: Chain E: N.295, Y.331 Chain F: 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 F, 2 interactions with chain E Hydrogen bonds: F:A.42, F:D.107, F:D.107, F:S.108, F:T.139, F:D.140, F:A.165, E:N.295 Water bridges: F:L.43, E:Y.331 ASN.32: 12 residues within 4Å: Chain G: G.41, A.42, M.45, D.107, S.108, G.138, T.139, D.140, A.165, Q.166 Chain H: N.295, Y.331 12 PLIP interactions: 9 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:A.42, G:D.107, G:S.108, G:T.139, G:D.140, G:D.140, G:A.165, H:N.295 Water bridges: G:L.43, G:Q.166, H:Y.331 Hydrophobic interactions: H:Y.331 ASN.38: 12 residues within 4Å: Chain G: N.295, Y.331 Chain H: G.41, A.42, M.45, D.107, S.108, G.138, T.139, D.140, A.165, Q.166 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:A.42, H:D.107, H:D.107, H:S.108, H:T.139, H:D.140, H:A.165, G:N.295 Water bridges: H:L.43

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

EDO.2: 7 residues within 4Å: Chain A: G.44, Q.46, G.55, P.56, G.57, L.58, R.170 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: E.154, Y.357, L.377, R.378 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: P.227, T.230, T.236, A.238 Ligand excluded by PLIP EDO.5: 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.7: 8 residues within 4Å: Chain B: N.224, S.320, Q.321, C.322, L.323, G.325, D.345, M.346 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain B: S.226, P.227, A.229, T.230, T.236, A.238 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: 3 residues within 4Å: Chain B: R.243, K.244, K.246 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain C: G.44, Q.46, G.55, P.56, G.57, L.58, R.170 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain C: E.154, Y.357, L.377, R.378 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain C: P.227, T.230, T.236, A.238 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain C: N.224, S.320, C.322, L.323, G.325, D.345, M.346 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain D: N.224, S.320, Q.321, C.322, L.323, G.325, D.345, M.346 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain D: S.226, P.227, A.229, T.230, T.236, A.238 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain D: E.154, Y.357, L.377, R.378 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain D: R.243, K.244, K.246 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain E: E.154, Y.357, R.378 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain E: S.226, P.227, A.229, T.230, T.236, A.238 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain E: N.224, S.320, C.322, L.323, G.325, D.345, M.346 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: D.301 Chain E: N.256, M.257, E.258, G.360 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain E: S.201, V.231, G.232 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain F: G.44, G.55, P.56, G.57, L.58, R.170 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain F: K.216, F.217, E.218 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain F: E.154, Y.357, L.377, R.378 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain F: N.224, S.320, C.322, L.323, G.325, D.345, M.346 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain G: E.154, Y.357, R.378 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain G: S.226, P.227, A.229, T.230, T.236, A.238 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain G: N.224, S.320, C.322, L.323, G.325, D.345, M.346 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain C: D.301 Chain G: N.256, M.257, E.258, G.360 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain G: S.201, V.231, G.232 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain H: G.44, G.55, P.56, G.57, L.58, R.170 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain H: K.216, F.217, E.218 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain H: E.154, Y.357, L.377, R.378 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain H: 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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
B

D
C

E
A

F
D

G
A

H
D

L-asparaginase

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