SMTL ID : 6nxd.1

TYPE I L-ASPARAGINASE FROM ESCHERICHIA COLI IN COMPLEX WITH CITRATE AT PH 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

10 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.3: 3 residues within 4Å: Chain A: N.127, G.218 Ligands: EDO.7 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: Q.89, H.90, E.93 Ligand excluded by PLIP CL.10: 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.11: 6 residues within 4Å: Chain B: H.185, A.186, D.187, G.188 Chain D: S.295, G.296 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: K.23, K.24, P.67 Ligands: EDO.17 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: G.220, E.221 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain C: N.127, G.218 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain D: K.23, K.24, P.67 Ligands: EDO.30 Ligand excluded by PLIP

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5: 11 residues within 4Å: Chain A: G.33, T.34, M.37, D.79, S.80, S.81, G.110, T.111, D.112, S.137 Chain C: N.266 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.34, A:D.79, A:S.80, A:S.81, A:S.81, A:T.111, A:D.112 Water bridges: A:I.35 CIT.14: 11 residues within 4Å: Chain B: G.33, T.34, M.37, D.79, S.80, S.81, G.110, T.111, D.112, S.137 Chain D: N.266 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:T.34, B:S.80, B:S.81, B:S.81, B:T.111, B:D.112, B:D.112, D:N.266 Water bridges: B:I.35 CIT.20: 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, S.137 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.34, C:D.79, C:S.80, C:S.81, C:S.81, C:T.111, C:D.112, C:D.112, A:N.266 Water bridges: C:S.137 CIT.25: 12 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, S.137 Ligands: EDO.28 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:T.34, D:S.80, D:S.80, D:S.81, D:S.81, D:T.111, D:D.112, D:D.112, D:D.112 Water bridges: D:T.111, D:S.137

4 x ASN: ASPARAGINE(Non-covalent)

ASN.6: 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.8, EDO.23 9 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions, 3 interactions with chain C Hydrogen bonds: A:T.182, A:T.291, A:V.322, A:E.323, N.6 Salt bridges: A:R.260, C:R.260 Water bridges: C:R.260, C:Q.292 ASN.15: 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.16, EDO.31 8 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions, 2 interactions with chain D Hydrogen bonds: B:T.182, B:T.291, B:V.322, B:E.323, N.15 Salt bridges: B:R.260, D:R.260 Water bridges: D:R.260 ASN.21: 11 residues within 4Å: Chain A: R.260 Chain C: T.182, R.260, T.291, Q.292, C.293, T.321, V.322, E.323 Ligands: EDO.9, EDO.22 8 PLIP interactions: 5 interactions with chain C, 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: C:T.291, C:V.322, C:E.323, N.21 Water bridges: C:R.260, A:R.260 Salt bridges: C:R.260, A:R.260 ASN.26: 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.18, EDO.27 8 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: D:T.291, D:T.291, D:V.322, D:E.323, N.26 Salt bridges: D:R.260, B:R.260 Water bridges: B:R.260

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

EDO.7: 7 residues within 4Å: Chain A: N.165, E.166, A.215, P.216, H.217, R.351 Ligands: CL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.165 Water bridges: A:L.128, A:V.167 EDO.8: 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.6 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: N.6, A:N.196, A:G.296 EDO.9: 8 residues within 4Å: Chain A: T.236, R.260, Q.292 Chain C: Y.116, R.260, V.322, E.323 Ligands: ASN.21 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.260, A:R.260, C:R.260 Water bridges: A:Q.292, A:Q.292, C:T.182 EDO.16: 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.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.196, B:G.296 Water bridges: B:V.322 EDO.17: 7 residues within 4Å: Chain B: H.20, Q.22, K.23, P.64, E.65, M.66 Ligands: CL.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.20, B:M.66 Water bridges: B:K.24 EDO.18: 8 residues within 4Å: Chain B: T.236, R.260, Q.292 Chain D: Y.116, R.260, V.322, E.323 Ligands: ASN.26 6 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain D Hydrogen bonds: B:R.260, B:R.260 Water bridges: B:Q.292, B:Q.292, N.26, D:T.182 EDO.22: 10 residues within 4Å: Chain C: N.196, T.291, C.293, M.294, S.295, G.296, D.319, M.320, T.321 Ligands: ASN.21 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:N.196, C:G.296, N.21 Water bridges: C:V.322 EDO.23: 8 residues within 4Å: Chain A: Y.116, R.260, V.322, E.323 Chain C: T.236, R.260, Q.292 Ligands: ASN.6 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.27: 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.26 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:N.196, D:G.296, N.26, N.26 EDO.28: 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: CIT.25 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 EDO.29: 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.30: 6 residues within 4Å: Chain D: H.20, K.23, P.64, E.65, M.66 Ligands: CL.24 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.20, D:P.64 EDO.31: 8 residues within 4Å: Chain B: Y.116, R.260, V.322, E.323 Chain D: T.236, R.260, Q.292 Ligands: ASN.15 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Water bridges: B:T.182, B:T.182, B:E.323, D:Q.292 Hydrogen bonds: D:R.260, D:R.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lubkowski, J. et al., Opportunistic complexes of E. coli L-asparaginases with citrate anions. Sci Rep (2019)

Release Date

2019-08-07

Peptides

L-asparaginase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-asparaginase 1

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