SMTL ID : 6nxc.1

ECAI(T162A) MUTANT IN COMPLEX WITH CITRATE AT PH 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

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

CIT.1: 12 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 Ligands: GOL.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.34, A:S.80, A:S.80, A:S.81, A:S.81, A:T.111, A:D.112 Water bridges: A:I.35 CIT.10: 12 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 Ligands: EDO.14 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain B Hydrogen bonds: D:N.266, B:T.34, B:D.79, B:S.80, B:S.81, B:S.81, B:T.111, B:D.112, B:D.112 Water bridges: B:I.35, B:T.111 CIT.20: 12 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 Ligands: EDO.22 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:I.35 CIT.26: 13 residues within 4Å: Chain B: N.266, Y.303 Chain D: G.33, T.34, M.37, D.79, S.80, S.81, G.110, T.111, D.112, S.137 Ligands: EDO.30 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain B 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:I.35, D:T.111 Hydrophobic interactions: B:Y.303, B:Y.303

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

EDO.2: 3 residues within 4Å: Chain A: H.72, D.94, H.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.72, A:D.94 EDO.3: 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.9 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: N.9, A:N.196, A:G.296 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.19 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.260, A:R.260, A:R.260 Water bridges: C:E.323, A:Q.292 EDO.12: 7 residues within 4Å: Chain B: H.20, Q.22, K.23, P.64, E.65, M.66 Ligands: CL.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.20, B:M.66 Water bridges: B:N.161 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.11 5 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain B Hydrogen bonds: N.11, N.11, B:N.196, B:G.296 Water bridges: B:V.322 EDO.14: 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: CIT.10 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.18: 8 residues within 4Å: Chain A: Y.116, R.260, V.322, E.323 Chain C: T.236, R.260, Q.292 Ligands: ASN.9 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.260, C:R.260, A:R.260 Water bridges: C:Q.292, A:E.323 EDO.21: 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.19 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:N.196, C:G.296, N.19 Water bridges: C:V.322 EDO.22: 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: CIT.20 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.29: 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.25 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Ligand interactions Hydrogen bonds: D:N.196, D:G.296, N.25, N.25 Water bridges: N.25 EDO.30: 10 residues within 4Å: Chain B: G.263, V.264, N.266, Y.303 Chain C: I.205 Chain D: D.112, Q.138, K.183, A.186 Ligands: CIT.26 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:D.112, D:Q.138, D:K.183, D:A.186, B:V.264, B:N.266

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

CL.4: 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.6: 2 residues within 4Å: Chain A: N.127, G.218 Ligand excluded by PLIP CL.8: 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.15: 4 residues within 4Å: Chain B: K.23, K.24, P.67 Ligands: EDO.12 Ligand excluded by PLIP CL.16: 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.17: 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.23: 3 residues within 4Å: Chain C: Q.89, H.90, E.93 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain D: R.53 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain D: K.23, K.24, P.67 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain D: G.220, E.221 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.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: CIT.1 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Q.138, A:K.183, A:A.186, C:Y.262, C:V.264, C:N.266

4 x ASN: ASPARAGINE(Non-covalent)

ASN.9: 11 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.3, EDO.18 6 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions, 4 interactions with chain A Salt bridges: C:R.260, A:R.260 Hydrogen bonds: N.9, A:T.291, A:V.322, A:E.323 ASN.11: 11 residues within 4Å: Chain B: A.182, R.260, T.291, Q.292, C.293, M.294, T.321, V.322, E.323 Chain D: R.260 Ligands: EDO.13 9 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions, 4 interactions with chain D Hydrogen bonds: B:T.291, B:V.322, B:E.323, N.11 Salt bridges: B:R.260, D:R.260 Water bridges: D:R.260, D:R.260, D:R.260 ASN.19: 11 residues within 4Å: Chain A: R.260 Chain C: A.182, R.260, T.291, Q.292, C.293, T.321, V.322, E.323 Ligands: EDO.7, EDO.21 6 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C, 1 Ligand-Ligand interactions Salt bridges: A:R.260, C:R.260 Hydrogen bonds: C:T.291, C:V.322, C:E.323, N.19 ASN.25: 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.29 9 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain D, 3 interactions with chain B Hydrogen bonds: N.25, 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

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