SMTL ID : 5gx8.3 (2 other biounits)

Crystal structure of solute-binding protein related to glycosaminoglycans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.163, N.165, N.167, K.169, D.171, E.172 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.163, A:K.169, A:D.171, A:E.172, A:E.172 CA.9: 6 residues within 4Å: Chain B: D.163, N.165, N.167, K.169, D.171, E.172 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.163, B:K.169, B:D.171, B:E.172, B:E.172

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

EDO.2: 6 residues within 4Å: Chain A: N.124, I.125, L.385, Y.396, K.397, M.400 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.397 EDO.3: 7 residues within 4Å: Chain A: K.194, A.195, S.196, Y.200, Q.212, E.214, R.293 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.195, A:E.214, A:R.293 Water bridges: A:F.215 EDO.4: 5 residues within 4Å: Chain A: R.183, P.197, Y.208, R.430, E.434 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.183, A:Y.208, A:Y.208, A:E.434 EDO.10: 5 residues within 4Å: Chain A: K.416 Chain B: R.238, E.241, Y.245 Ligands: SO4.15 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.416, B:R.238, B:E.241 Water bridges: A:D.68 EDO.11: 7 residues within 4Å: Chain B: K.194, A.195, S.196, Y.200, Q.212, E.214, R.293 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.214, B:E.214, B:R.293, B:R.293 EDO.12: 6 residues within 4Å: Chain B: E.64, L.65, S.66, Y.299, L.300, G.301 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.66, B:G.301 Water bridges: B:S.66 EDO.13: 7 residues within 4Å: Chain B: R.101, Y.122, A.295, R.296, T.298, D.407, E.408 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.101, B:R.101, B:E.408 EDO.14: 3 residues within 4Å: Chain B: N.165, N.167, N.250 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.250

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

SO4.5: 4 residues within 4Å: Chain A: R.238, Y.245 Chain B: K.416, K.420 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.416, B:K.420, A:R.238 SO4.6: 3 residues within 4Å: Chain A: N.181, R.183, R.430 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.181 Salt bridges: A:R.183, A:R.430 SO4.7: 2 residues within 4Å: Chain A: S.38, Q.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.39 Water bridges: A:Q.39 SO4.8: 2 residues within 4Å: Chain A: H.217, K.220 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.217, A:K.220 SO4.15: 6 residues within 4Å: Chain A: K.416, K.420 Chain B: E.234, R.238, Y.245 Ligands: EDO.10 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.416, A:K.420, B:R.238 Water bridges: B:R.238 SO4.16: 2 residues within 4Å: Chain B: H.217, K.220 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.217, B:K.220 SO4.17: 2 residues within 4Å: Chain B: S.38, Q.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.39 Water bridges: B:Q.39

1 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.18: 4 residues within 4Å: Chain B: R.178, R.243, W.258, S.261 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.178, B:S.261, B:S.261 Water bridges: B:S.261, A:Q.46 Salt bridges: B:R.178, B:R.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oiki, S. et al., A bacterial ABC transporter enables import of mammalian host glycosaminoglycans. Sci Rep (2017)

Release Date

2017-07-19

Peptides

Extracellular solute-binding protein family 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Extracellular solute-binding protein family 1

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