SMTL ID : 6aa1.1

Crystal structure of putative amino acid binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus bound with citrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: Q.83, Y.86, D.87, F.88 Chain B: R.205, N.208 Ligands: EDO.37 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.83, A:D.87, A:F.88, A:F.88, B:R.205 Water bridges: A:Q.83 GOL.22: 5 residues within 4Å: Chain A: D.15, I.17, A.57, V.58, H.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.15, A:V.58 Water bridges: A:S.59 GOL.23: 6 residues within 4Å: Chain A: F.23, N.168, E.171, R.172, Y.227 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.168, A:E.171, A:R.172 GOL.24: 7 residues within 4Å: Chain A: M.186, K.187, D.188, N.189, S.190 Chain B: L.216, C.239 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.187, A:D.188, A:N.189 Water bridges: B:C.239 GOL.43: 7 residues within 4Å: Chain B: P.19, P.20, F.23, N.168, R.172, Y.227 Ligands: GOL.44 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.168, B:Y.227 GOL.44: 9 residues within 4Å: Chain B: P.20, I.164, N.168, E.171, Y.227, F.228, D.229, I.233 Ligands: GOL.43 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.164, B:N.168, B:N.168, B:D.229, B:D.229 GOL.45: 4 residues within 4Å: Chain B: H.142, N.143, E.145, Q.146 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.142, B:N.143

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

EDO.2: 2 residues within 4Å: Chain A: K.222, R.226 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: E.42, K.222, I.223, R.226 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: I.182, A.183, D.184, R.185 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: T.14, D.15, Y.18, V.74, N.75 Ligands: EDO.18 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: T.33, R.226, Y.227 Ligands: GOL.23 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: F.53, E.55 Ligands: EDO.8, EDO.9 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Ligands: EDO.7, EDO.9 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: H.24, E.31, L.32 Ligands: EDO.7, EDO.8 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: G.199, N.200, N.201, K.202 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: D.15, G.16, I.17, H.24, E.55 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: P.19, F.23, H.24, D.27, G.28 Ligands: EDO.20 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: D.126, R.129, F.130, E.133 Chain B: S.241 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: C.239, S.240 Chain B: M.186, K.187, D.188, S.190 Ligands: EDO.25 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: S.110, F.111, K.112, D.184 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: P.19, F.144, E.145, P.165, N.168, F.169, R.172 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: R.197, K.198 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: Y.18, V.58, N.75, T.125, F.144 Ligands: EDO.5, CIT.21 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain A: P.174, H.175 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: I.17, P.19, N.143, E.145 Ligands: EDO.12 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain A: S.240, S.241 Chain B: D.126, L.127, M.186 Ligands: EDO.14, CIT.42 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain A: N.189, S.234 Chain B: S.235, V.236, P.237 Ligands: EDO.27 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: P.237 Chain B: N.189, S.235, V.236 Ligands: EDO.26 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: S.103, G.177, N.178, F.180, K.181 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain B: Y.220, K.221, F.224, D.225, K.230, S.235 Ligands: EDO.35 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain B: T.14, D.15, Y.18, H.21, V.74, N.75 Ligands: EDO.38 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain B: T.56, G.60, T.63, G.64, T.67, R.69 Ligands: PEG.46 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain A: R.205, N.208 Chain B: Q.83, Y.86, F.88 Ligands: EDO.37 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: E.171, D.225, Y.227, F.228, D.229 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain B: E.42, K.222, I.223, R.226 Ligand excluded by PLIP EDO.35: 8 residues within 4Å: Chain A: D.188 Chain B: I.214, H.215, G.218, T.219, Y.220, K.221 Ligands: EDO.29 Ligand excluded by PLIP EDO.36: 2 residues within 4Å: Chain B: D.27, G.28 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain A: T.204 Chain B: D.87, F.88 Ligands: GOL.1, EDO.32 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain B: Y.18, V.58, N.75, F.144 Ligands: EDO.30, CIT.42 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain B: G.199, N.200, N.201, K.202 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain B: I.17, A.57, H.142 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain B: H.45, N.48, L.49 Ligand excluded by PLIP

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

CIT.21: 11 residues within 4Å: Chain A: A.77, R.82, H.95, T.125, D.126, L.127, F.144, P.162, S.190 Chain B: S.240 Ligands: EDO.18 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.125, A:D.126, A:L.127, A:S.190, A:S.190, B:S.240 Water bridges: A:R.82, A:D.126 Salt bridges: A:R.82, A:H.95 CIT.42: 13 residues within 4Å: Chain A: S.240 Chain B: A.77, R.82, H.95, V.97, T.125, D.126, L.127, F.144, P.162, S.190 Ligands: EDO.25, EDO.38 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.77, B:T.125, B:D.126, B:L.127, B:S.190, A:S.240 Water bridges: B:R.82, B:S.128 Salt bridges: B:R.82, B:H.95

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.46: 5 residues within 4Å: Chain B: T.56, A.57, S.59, G.60 Ligands: EDO.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.57 Water bridges: B:S.59

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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