SMTL ID : 6aal.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: E.171, R.226, Y.227, F.228, D.229 No protein-ligand interaction detected (PLIP) EDO.5: 4 residues within 4Å: Chain A: S.8, N.48, L.49, K.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.8 EDO.6: 3 residues within 4Å: Chain A: V.58, L.61 Ligands: ARG.4 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: R.4, A:R.82 EDO.7: 5 residues within 4Å: Chain A: T.14, D.15, Y.18, V.74, N.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.14, A:D.15, A:N.75 EDO.8: 1 residues within 4Å: Chain A: R.29 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: N.68, R.197, N.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.68, A:R.197, A:N.200 EDO.10: 9 residues within 4Å: Chain A: I.90, P.91, L.211, C.212, H.215, P.237, G.238, C.239 Chain B: A.191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.238 EDO.11: 2 residues within 4Å: Chain A: S.136, H.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.136, A:H.137 EDO.12: 2 residues within 4Å: Chain A: A.25, Q.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.26 EDO.13: 2 residues within 4Å: Chain A: E.42, R.226 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.226, A:R.226 Water bridges: A:K.222, A:K.222 EDO.17: 2 residues within 4Å: Chain B: P.174, H.175 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.175

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

SO4.2: 5 residues within 4Å: Chain A: R.172, 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 SO4.3: 3 residues within 4Å: Chain A: H.24, E.31, L.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.24, A:L.32, A:L.32 SO4.15: 9 residues within 4Å: Chain B: V.58, Q.121, L.123, G.124, T.125, D.126, L.127, S.128, F.140 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.121, B:G.124, B:D.126, B:L.127 SO4.16: 2 residues within 4Å: Chain B: S.234, S.235 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.235

1 x ARG: ARGININE(Non-covalent)

ARG.4: 11 residues within 4Å: Chain A: A.77, R.82, H.95, V.97, T.125, D.126, L.127, S.190 Chain B: S.240 Ligands: EDO.6, ACT.14 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.77 Hydrogen bonds: A:H.95, A:D.126, A:L.127, A:S.190, B:S.240 Salt bridges: A:R.82

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

ACT.14: 6 residues within 4Å: Chain A: V.97, M.186, S.190 Chain B: S.240, S.241 Ligands: ARG.4 3 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: A:S.190 Salt bridges: R.4 Water bridges: B:S.241 ACT.18: 2 residues within 4Å: Chain B: K.222, R.226 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.222 Salt bridges: B:K.222, B:R.226 ACT.19: 5 residues within 4Å: Chain B: I.90, H.215, P.237, G.238, C.239 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.90 Salt bridges: B:H.215 ACT.20: 5 residues within 4Å: Chain B: E.171, D.225, Y.227, F.228, D.229 No protein-ligand interaction detected (PLIP) ACT.21: 2 residues within 4Å: Chain B: I.62, R.82 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.82 Salt bridges: B:R.82, B:R.129

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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