SMTL ID : 7wsu.1

Cryo-EM structure of the barley Yellow stripe 1 transporter in complex with Fe(III)-PDMA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 5 residues within 4Å: Chain A: A.262, Q.265, F.267, G.299, P.303 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.262, A:F.267, A:F.267, A:P.303 Y01.4: 9 residues within 4Å: Chain A: T.257, F.258, G.259, L.260, P.676 Chain B: F.239, F.243, P.669, I.670 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.239, B:F.243, B:F.243, B:F.243, B:F.243, B:P.669, B:P.669, B:I.670, B:I.670, A:L.260 Y01.5: 9 residues within 4Å: Chain A: F.239, F.243, P.669, I.670 Chain B: T.257, F.258, G.259, L.260, P.676 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.239, A:F.243, A:F.243, A:F.243, A:F.243, A:P.669, A:P.669, A:I.670, A:I.670, B:L.260 Y01.6: 5 residues within 4Å: Chain B: A.262, Q.265, F.267, G.299, P.303 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.262, B:F.267, B:F.267, B:P.303

2 x FE: FE (III) ION(Non-covalent)

FE.2: 2 residues within 4Å: Chain A: K.482 Ligands: 5ZS.3 No protein-ligand interaction detected (PLIP) FE.7: 2 residues within 4Å: Chain B: K.482 Ligands: 5ZS.8 No protein-ligand interaction detected (PLIP)

2 x 5ZS: (2~{S})-1-[(3~{S})-3-[[(3~{S})-3,4-bis(oxidanyl)-4-oxidanylidene-butyl]amino]-4-oxidanyl-4-oxidanylidene-butyl]pyrrolidine-2-carboxylic acid(Non-covalent)

5ZS.3: 14 residues within 4Å: Chain A: G.76, V.78, F.130, G.133, F.134, G.135, S.136, Y.451, K.455, K.482, L.486, Y.547, Y.551 Ligands: FE.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.78, A:F.130 Hydrogen bonds: A:G.135, A:S.136, A:S.136, A:Y.551 Salt bridges: A:K.455, A:K.482, A:K.482, A:K.482 5ZS.8: 14 residues within 4Å: Chain B: G.76, V.78, F.130, G.133, F.134, G.135, S.136, Y.451, K.455, K.482, L.486, Y.547, Y.551 Ligands: FE.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.78, B:F.130 Hydrogen bonds: B:G.135, B:S.136, B:S.136, B:Y.551 Salt bridges: B:K.455, B:K.482, B:K.482, B:K.482

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamagata, A. et al., Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter. Nat Commun (2022)

Release Date

2022-11-30

Peptides

Iron-phytosiderophore transporter: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Iron-phytosiderophore transporter

Related Entries With Identical Sequence