SMTL ID : 6a80.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: I.17, P.19, N.143, E.145 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: A.57, V.58, S.59, I.122, L.123, S.141 Ligands: ACT.5 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: I.17, H.24, E.55 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: T.14, D.15, Y.18, V.74, N.75 Ligands: EDO.14 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: R.96, L.98, F.167, R.185, I.232 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Chain A: F.140 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: Y.18, N.75, T.125, F.144 Ligands: EDO.11, CYS.19 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: N.201 Chain B: N.201 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: V.139, F.140, Q.146, R.155 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: S.241 Chain B: D.126, L.127, R.129, F.130, M.186 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: P.19, F.23, N.168, R.172 Ligands: TRS.4 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: L.127, F.130 Chain B: S.240, S.241 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain B: Y.18, V.58, N.75, F.144 Ligands: EDO.26, CYS.32, CYS.33 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: T.14, D.15, L.61, N.75 Ligands: EDO.25 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain B: T.56, G.60, T.63, G.64, T.67, R.69 Ligands: EDO.29 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: E.31, L.32, F.53 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain B: T.56, A.57, G.60 Ligands: EDO.27 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: I.17, P.19, F.23, N.143, E.145 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: E.171, D.225, Y.227, F.228, D.229 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.171, A:E.171, A:D.225 Water bridges: A:N.168, A:N.168, A:Y.227 GOL.15: 3 residues within 4Å: Chain A: R.96, R.185 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.96, A:R.185, A:R.185 GOL.16: 2 residues within 4Å: Chain A: N.231 Ligands: GOL.15 No protein-ligand interaction detected (PLIP) GOL.30: 4 residues within 4Å: Chain A: N.189 Chain B: S.235, V.236, P.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.189

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

TRS.4: 5 residues within 4Å: Chain A: F.23, A.25, Q.26, D.27 Ligands: EDO.22 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.26, A:D.27, A:D.27 Water bridges: A:T.33

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

ACT.5: 5 residues within 4Å: Chain A: D.15, I.17, A.57, H.142 Ligands: EDO.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.57, A:H.142 Water bridges: A:V.58 ACT.6: 5 residues within 4Å: Chain A: K.221, F.224, D.225, K.230, S.235 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.230 Salt bridges: A:K.221 ACT.7: 2 residues within 4Å: Chain A: K.222, R.226 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.222, A:R.226 ACT.8: 5 residues within 4Å: Chain A: R.172, R.173, P.174, H.175, D.176 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.175, A:D.176, A:D.176 Salt bridges: A:H.175 ACT.9: 5 residues within 4Å: Chain A: K.230, N.231, I.232, I.233, S.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.231 Water bridges: A:S.235 ACT.24: 4 residues within 4Å: Chain A: N.201, R.205 Chain B: G.199, N.201 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.201, B:N.201 Salt bridges: A:R.205, B:K.198

4 x CYS: CYSTEINE(Non-covalent)

CYS.19: 9 residues within 4Å: Chain A: N.75, V.76, A.77, R.82, H.95, T.125, D.126 Ligands: EDO.14, CYS.20 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:N.75, A:A.77, A:R.82, C.19, C.19 Water bridges: A:H.95 Salt bridges: A:R.82, A:H.95 CYS.20: 6 residues within 4Å: Chain A: I.62, R.82, G.124, T.125, D.126 Ligands: CYS.19 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:G.124, C.20, C.20 Water bridges: A:I.62, C.19 Salt bridges: A:R.82 CYS.32: 9 residues within 4Å: Chain B: N.75, V.76, A.77, R.82, H.95, T.125, D.126 Ligands: EDO.25, CYS.33 9 PLIP interactions: 4 Ligand-Ligand interactions, 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C.33, C.33, B:A.77, B:R.82 Water bridges: C.32, C.32, A:S.240 Salt bridges: B:R.82, B:H.95 CYS.33: 9 residues within 4Å: Chain B: V.58, L.61, N.75, V.76, R.82, T.125, D.126 Ligands: EDO.25, CYS.32 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Water bridges: B:L.61, B:L.61 Salt bridges: B:R.82 Hydrogen bonds: C.32, C.32

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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