SMTL ID : 6a8s.1

Crystal Structure of the putative amino acid-binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Cysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: K.222, R.226 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.226 SO4.19: 2 residues within 4Å: Chain B: K.222, R.226 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.222, B:R.226 SO4.20: 2 residues within 4Å: Chain B: E.133, K.135 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.135

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

EDO.2: 7 residues within 4Å: Chain A: Y.18, V.58, N.75, T.125, F.144 Ligands: EDO.5, CYS.15 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: E.42, K.222, R.226 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: T.14, D.15, Y.18, V.74, N.75 Ligands: EDO.2 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: T.67, R.69 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: Y.220, K.221, F.224, D.225, K.230 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: H.24, F.53, E.55 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: R.172, R.173 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: D.15, G.16, H.24, E.55 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: S.234, S.235 Ligand excluded by PLIP EDO.12: 1 residues within 4Å: Chain A: D.116 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: S.241 Chain B: L.127, F.130, M.186 Ligands: EDO.17 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain A: S.240 Chain B: A.77, H.95, V.97, L.127, S.190 Ligands: EDO.16, CYS.33 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: A.77, H.95, V.97, L.127, S.190 Chain B: S.240 Ligands: CYS.15 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: V.58, N.75, T.125, F.144 Ligands: EDO.24, EDO.29, CYS.33 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: E.42, T.219, K.222, I.223, R.226 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain B: V.58, I.62, N.75, V.76, R.82 Ligands: EDO.21, EDO.28, CYS.33 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: T.56, G.60, T.63, G.64, T.67, R.69 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain B: Q.105, Q.106 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: A.25, Q.26, D.27 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain B: V.58, L.61, I.62, R.82, G.124, T.125 Ligands: EDO.24, CYS.33 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain B: T.14, D.15, H.21, S.22, L.61, N.75 Ligands: EDO.21 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: F.54, E.55, T.56, R.69 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 3 residues within 4Å: Chain A: A.25, Q.26, D.27 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.26, A:Q.26, A:D.27 Water bridges: A:G.28, A:G.28

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 4 residues within 4Å: Chain A: R.173, P.174, H.175, D.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.175, A:D.176 Salt bridges: A:H.175 ACT.22: 4 residues within 4Å: Chain B: K.132, K.135, S.136 Ligands: GOL.32 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.135 ACT.31: 2 residues within 4Å: Chain B: E.31, L.32 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.31 Hydrogen bonds: B:L.32 Salt bridges: B:H.24

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 5 residues within 4Å: Chain A: R.96, D.163, F.167, R.185, I.232 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.163, A:R.185, A:I.232 GOL.32: 4 residues within 4Å: Chain B: S.136, H.137, L.138 Ligands: ACT.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.138

2 x CYS: CYSTEINE(Non-covalent)

CYS.15: 7 residues within 4Å: Chain A: A.77, R.82, T.125, D.126, L.127 Ligands: EDO.2, EDO.18 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:D.126, A:L.127, C.15, C.15 Salt bridges: A:R.82 CYS.33: 9 residues within 4Å: Chain B: A.77, R.82, T.125, D.126, L.127 Ligands: EDO.17, EDO.21, EDO.24, EDO.28 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.126, B:L.127 Water bridges: B:R.82 Salt bridges: B:R.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, P. et al., Crystal structures of a putative periplasmic cystine-binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding. Febs J. (2019)

Release Date

2019-06-12

Peptides

Putative amino acid-binding periplasmic ABC transporter protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative amino acid-binding periplasmic ABC transporter protein

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