SMTL ID : 2him.1

Crystal Structure and Allosteric Regulation of the Cytoplasmic Escherichia coli L-Asparaginase I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-tetramer

Ligands

4 x ASP: ASPARTIC ACID(Covalent)

ASP.1: 11 residues within 4Å: Chain A: G.33, T.34, D.79, S.80, G.110, T.111, D.112, S.137 Chain C: N.266 Ligands: ASN.3, EDO.5 9 PLIP interactions: 6 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:T.34, A:S.80, A:T.111, A:D.112, A:D.112, N.3, N.3 Water bridges: A:I.35 Hydrophobic interactions: N.3 ASP.6: 11 residues within 4Å: Chain B: G.33, T.34, D.79, S.80, G.110, T.111, D.112, S.137 Chain D: N.266 Ligands: ASN.8, EDO.10 10 PLIP interactions: 7 interactions with chain B, 3 Ligand-Ligand interactions Hydrogen bonds: B:T.34, B:S.80, B:T.111, B:D.112, B:D.112, N.8, N.8 Water bridges: B:T.111, B:S.137 Hydrophobic interactions: N.8 ASP.11: 12 residues within 4Å: Chain A: N.266 Chain C: G.33, T.34, D.79, S.80, S.81, G.110, T.111, D.112, S.137 Ligands: ASN.13, EDO.15 10 PLIP interactions: 3 Ligand-Ligand interactions, 7 interactions with chain C Hydrophobic interactions: N.13 Hydrogen bonds: N.13, N.13, C:T.34, C:S.80, C:S.81, C:T.111, C:D.112, C:D.112 Water bridges: C:I.35 ASP.16: 11 residues within 4Å: Chain B: N.266 Chain D: G.33, T.34, D.79, S.80, G.110, T.111, D.112, S.137 Ligands: ASN.18, EDO.20 10 PLIP interactions: 7 interactions with chain D, 3 Ligand-Ligand interactions Hydrogen bonds: D:T.34, D:S.80, D:T.111, D:D.112, D:D.112, N.18, N.18 Water bridges: D:I.35, D:T.111 Hydrophobic interactions: N.18

8 x ASN: ASPARAGINE(Non-covalent)

ASN.2: 10 residues within 4Å: Chain A: A.182, R.260, T.291, Q.292, C.293, T.321, V.322, E.323 Chain C: R.260 Ligands: EDO.4 10 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: A:T.291, A:T.291, A:V.322, A:E.323, N.2 Salt bridges: A:R.260, C:R.260 Water bridges: C:R.260, C:R.260, C:R.260 ASN.3: 11 residues within 4Å: Chain A: G.33, T.34, M.37, D.79, S.80, S.81, G.110, T.111, D.112 Chain C: N.266 Ligands: ASP.1 11 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C, 5 Ligand-Ligand interactions Hydrogen bonds: A:T.34, A:S.80, A:S.81, A:S.81, A:D.112, C:N.266, D.1, D.1, N.3, N.3 Hydrophobic interactions: D.1 ASN.7: 10 residues within 4Å: Chain B: A.182, R.260, T.291, Q.292, C.293, T.321, V.322, E.323 Chain D: R.260 Ligands: EDO.9 9 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions, 3 interactions with chain D Hydrogen bonds: B:T.291, B:T.291, B:V.322, B:E.323, N.7 Salt bridges: B:R.260, D:R.260 Water bridges: D:R.260, D:R.260 ASN.8: 11 residues within 4Å: Chain B: G.33, T.34, M.37, D.79, S.80, S.81, G.110, T.111, D.112 Chain D: N.266 Ligands: ASP.6 12 PLIP interactions: 7 interactions with chain B, 5 Ligand-Ligand interactions Hydrogen bonds: B:T.34, B:S.80, B:S.81, B:S.81, B:S.81, B:D.112, B:D.112, D.6, D.6, N.8, N.8 Hydrophobic interactions: D.6 ASN.12: 11 residues within 4Å: Chain A: R.260 Chain C: A.182, R.260, T.291, Q.292, C.293, M.294, T.321, V.322, E.323 Ligands: EDO.14 9 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain C, 3 interactions with chain A Hydrogen bonds: N.12, C:T.291, C:T.291, C:V.322, C:E.323 Salt bridges: C:R.260, A:R.260 Water bridges: A:R.260, A:R.260 ASN.13: 11 residues within 4Å: Chain A: N.266 Chain C: G.33, T.34, M.37, D.79, S.80, S.81, G.110, T.111, D.112 Ligands: ASP.11 13 PLIP interactions: 5 Ligand-Ligand interactions, 8 interactions with chain C Hydrophobic interactions: D.11 Hydrogen bonds: D.11, D.11, N.13, N.13, C:T.34, C:D.79, C:S.80, C:S.81, C:S.81, C:S.81, C:T.111, C:D.112 ASN.17: 10 residues within 4Å: Chain B: R.260 Chain D: A.182, R.260, T.291, Q.292, C.293, T.321, V.322, E.323 Ligands: EDO.19 9 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain D, 3 interactions with chain B Hydrogen bonds: N.17, D:T.291, D:T.291, D:V.322, D:E.323 Salt bridges: D:R.260, B:R.260 Water bridges: B:R.260, B:R.260 ASN.18: 11 residues within 4Å: Chain B: N.266 Chain D: G.33, T.34, M.37, D.79, S.80, S.81, G.110, T.111, D.112 Ligands: ASP.16 12 PLIP interactions: 5 Ligand-Ligand interactions, 7 interactions with chain D Hydrophobic interactions: D.16 Hydrogen bonds: D.16, D.16, N.18, N.18, D:T.34, D:S.80, D:S.81, D:S.81, D:S.81, D:D.112, D:D.112

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

EDO.4: 10 residues within 4Å: Chain A: N.196, T.291, C.293, M.294, S.295, G.296, D.319, M.320, T.321 Ligands: ASN.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:N.196, A:G.296, N.2 Water bridges: N.2 EDO.5: 9 residues within 4Å: Chain A: D.112, Q.138, K.183, A.186 Chain B: I.205 Chain C: G.263, V.264, N.266 Ligands: ASP.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.112, A:K.183, A:A.186, C:V.264, C:N.266 EDO.9: 10 residues within 4Å: Chain B: N.196, T.291, C.293, M.294, S.295, G.296, D.319, M.320, T.321 Ligands: ASN.7 5 PLIP interactions: 3 Ligand-Ligand interactions, 2 interactions with chain B Hydrogen bonds: N.7, N.7, B:N.196, B:G.296 Water bridges: N.7 EDO.10: 9 residues within 4Å: Chain A: I.205 Chain B: D.112, Q.138, K.183, A.186 Chain D: G.263, V.264, N.266 Ligands: ASP.6 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:V.264, D:N.266, B:D.112, B:K.183, B:A.186 EDO.14: 11 residues within 4Å: Chain C: P.195, N.196, T.291, C.293, M.294, S.295, G.296, D.319, M.320, T.321 Ligands: ASN.12 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Ligand interactions Hydrogen bonds: C:N.196, C:G.296, N.12, N.12 Water bridges: N.12 EDO.15: 9 residues within 4Å: Chain A: G.263, V.264, N.266 Chain C: D.112, Q.138, K.183, A.186 Chain D: I.205 Ligands: ASP.11 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.112, C:K.183, C:A.186, A:V.264, A:N.266 EDO.19: 10 residues within 4Å: Chain D: N.196, T.291, C.293, M.294, S.295, G.296, D.319, M.320, T.321 Ligands: ASN.17 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain D Hydrogen bonds: N.17, D:N.196, D:G.296 Water bridges: D:T.291 EDO.20: 9 residues within 4Å: Chain B: G.263, V.264, N.266 Chain C: I.205 Chain D: D.112, Q.138, K.183, A.186 Ligands: ASP.16 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:V.264, B:N.266, D:D.112, D:K.183, D:A.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yun, M.K. et al., Crystal Structure and Allosteric Regulation of the Cytoplasmic Escherichia coli L-Asparaginase I. J.Mol.Biol. (2007)

Release Date

2007-05-15

Peptides

L-asparaginase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-asparaginase 1