SMTL ID : 2p2n.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 6 residues within 4Å: Chain A: S.295, G.296 Chain C: H.185, A.186, D.187, G.188 Ligand excluded by PLIP CL.2: 6 residues within 4Å: Chain A: H.185, A.186, D.187, G.188 Chain C: S.295, G.296 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: S.295, G.296 Chain D: H.185, A.186, D.187, G.188 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain B: H.185, A.186, D.187, G.188 Chain D: S.295, G.296 Ligand excluded by PLIP

4 x ASP: ASPARTIC ACID(Covalent)(Non-covalent)

ASP.3: 10 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.4 9 PLIP interactions: 5 interactions with chain A, 3 Ligand-Ligand interactions, 1 interactions with chain C Hydrogen bonds: A:T.34, A:S.80, A:T.111, A:D.112, N.4, N.4 Water bridges: A:I.35, C:N.266 Hydrophobic interactions: N.4 ASP.10: 8 residues within 4Å: Chain B: D.79, S.80, G.110, T.111, D.112, S.137 Chain D: N.266 Ligands: ASN.11 11 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D, 3 Ligand-Ligand interactions Hydrogen bonds: B:S.80, B:T.111, B:D.112, B:D.112, N.11, N.11 Water bridges: B:T.111, B:T.111, B:S.137, D:N.266 Hydrophobic interactions: N.11 ASP.16: 9 residues within 4Å: Chain A: N.266 Chain C: G.33, D.79, S.80, G.110, T.111, D.112, S.137 Ligands: ASN.17 7 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C, 2 Ligand-Ligand interactions Water bridges: A:N.266, N.17 Hydrogen bonds: C:S.80, C:T.111, C:D.112, C:D.112, N.17 ASP.21: 10 residues within 4Å: Chain B: N.266 Chain D: G.33, D.79, S.80, G.110, T.111, D.112, S.137 Ligands: ASN.22, EDO.25 10 PLIP interactions: 3 Ligand-Ligand interactions, 1 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: N.22 Hydrogen bonds: N.22, N.22, D:S.80, D:T.111, D:D.112, D:D.112 Water bridges: B:N.266, D:T.111, D:S.137

8 x ASN: ASPARAGINE(Non-covalent)

ASN.4: 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.3 12 PLIP interactions: 7 interactions with chain A, 5 Ligand-Ligand interactions Hydrogen bonds: A:D.79, A:S.80, A:S.81, A:S.81, A:S.81, A:T.111, A:D.112, D.3, D.3, N.4, N.4 Hydrophobic interactions: D.3 ASN.5: 11 residues within 4Å: Chain A: T.182, R.260, T.291, Q.292, C.293, T.321, V.322, E.323 Chain C: R.260 Ligands: EDO.6, EDO.20 10 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: A:T.182, A:T.291, A:T.291, A:V.322, A:E.323, N.5 Water bridges: A:R.260, C:R.260 Salt bridges: A:R.260, C:R.260 ASN.11: 9 residues within 4Å: Chain B: G.33, D.79, S.80, S.81, G.110, T.111, D.112 Chain D: N.266 Ligands: ASP.10 12 PLIP interactions: 6 interactions with chain B, 6 Ligand-Ligand interactions Hydrogen bonds: B:S.80, B:S.81, B:S.81, B:S.81, B:D.112, B:D.112, D.10, D.10, N.11, N.11, N.11 Hydrophobic interactions: D.10 ASN.12: 11 residues within 4Å: Chain B: T.182, R.260, T.291, Q.292, C.293, T.321, V.322, E.323 Chain D: R.260 Ligands: EDO.13, EDO.28 9 PLIP interactions: 6 interactions with chain B, 1 Ligand-Ligand interactions, 2 interactions with chain D Hydrogen bonds: B:T.182, B:T.291, B:T.291, B:V.322, B:E.323, N.12 Salt bridges: B:R.260, D:R.260 Water bridges: D:R.260 ASN.17: 9 residues within 4Å: Chain A: N.266 Chain C: G.33, D.79, S.80, S.81, G.110, T.111, D.112 Ligands: ASP.16 12 PLIP interactions: 5 interactions with chain C, 6 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: C:D.79, C:S.80, C:S.81, C:S.81, C:D.112, D.16, D.16, N.17, N.17, A:N.266 Hydrophobic interactions: D.16 Water bridges: D.16 ASN.18: 12 residues within 4Å: Chain A: R.260 Chain C: T.182, R.260, T.291, Q.292, C.293, M.294, T.321, V.322, E.323 Ligands: EDO.7, EDO.19 9 PLIP interactions: 6 interactions with chain C, 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: C:T.291, C:T.291, C:V.322, C:E.323, N.18 Water bridges: C:R.260, A:R.260 Salt bridges: C:R.260, A:R.260 ASN.22: 9 residues within 4Å: Chain B: N.266 Chain D: G.33, D.79, S.80, S.81, G.110, T.111, D.112 Ligands: ASP.21 11 PLIP interactions: 5 Ligand-Ligand interactions, 6 interactions with chain D Hydrophobic interactions: D.21 Hydrogen bonds: D.21, D.21, N.22, N.22, D:S.80, D:S.81, D:S.81, D:S.81, D:D.112, D:D.112 ASN.23: 11 residues within 4Å: Chain B: R.260 Chain D: T.182, R.260, T.291, Q.292, C.293, T.321, V.322, E.323 Ligands: EDO.15, EDO.24 8 PLIP interactions: 2 interactions with chain B, 5 interactions with chain D, 1 Ligand-Ligand interactions Water bridges: B:R.260 Salt bridges: B:R.260, D:R.260 Hydrogen bonds: D:T.291, D:T.291, D:V.322, D:E.323, N.23

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

EDO.6: 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.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:N.196, A:G.296, N.5 Water bridges: N.5 EDO.7: 8 residues within 4Å: Chain A: T.236, R.260, Q.292 Chain C: Y.116, R.260, V.322, E.323 Ligands: ASN.18 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:R.260, A:R.260, A:R.260 Water bridges: C:T.182, A:Q.292, A:Q.292 EDO.13: 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.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:N.196, B:G.296, N.12 Water bridges: N.12 EDO.14: 6 residues within 4Å: Chain B: H.20, Q.22, K.23, P.64, E.65, M.66 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.20, B:M.66 Water bridges: B:K.24, B:K.24 EDO.15: 8 residues within 4Å: Chain B: T.236, R.260, Q.292 Chain D: Y.116, R.260, V.322, E.323 Ligands: ASN.23 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.260, B:R.260 Water bridges: B:Q.292, B:Q.292, D:T.182 EDO.19: 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.18 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:N.196, C:G.296, N.18 Water bridges: N.18 EDO.20: 8 residues within 4Å: Chain A: Y.116, R.260, V.322, E.323 Chain C: T.236, R.260, Q.292 Ligands: ASN.5 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.260, C:R.260 Water bridges: C:Q.292, C:Q.292, A:T.182 EDO.24: 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.23 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain D Hydrogen bonds: N.23, D:N.196, D:G.296 EDO.25: 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.21 6 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 3 interactions with chain D Hydrogen bonds: B:V.264, B:N.266, D:D.112, D:K.183, D:A.186 Water bridges: D.21 EDO.26: 3 residues within 4Å: Chain D: P.16, N.165, H.217 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.165 EDO.27: 5 residues within 4Å: Chain D: H.20, K.23, P.64, E.65, M.66 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.20, D:P.64 EDO.28: 8 residues within 4Å: Chain B: Y.116, R.260, V.322, E.323 Chain D: T.236, R.260, Q.292 Ligands: ASN.12 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D Water bridges: B:T.182, B:T.182, B:E.323, D:Q.292, D:Q.292 Hydrogen bonds: D:R.260, D:R.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2007-05-15

Peptides

L-ASPARAGINASE I: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-ASPARAGINASE I

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