SMTL ID : 7wst.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 6 residues within 4Å: Chain A: K.261, A.262, Q.265, F.267, G.299, P.303 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.262, A:F.267, A:F.267, A:P.303 Hydrogen bonds: A:Q.265 Salt bridges: A:K.261 Y01.4: 9 residues within 4Å: Chain A: T.257, F.258, G.259, L.260, K.261, P.676 Chain B: F.243, P.669, I.670 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:L.260, B:F.243, B:F.243, B:F.243, B:F.243, B:P.669, B:P.669, B:I.670, B:I.670 Hydrogen bonds: A:L.260, A:K.261, B:P.669 Y01.5: 9 residues within 4Å: Chain A: F.243, P.669, I.670 Chain B: T.257, F.258, G.259, L.260, K.261, P.676 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: 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 Hydrogen bonds: A:P.669, B:L.260, B:K.261 Y01.6: 6 residues within 4Å: Chain B: K.261, A.262, Q.265, F.267, G.299, P.303 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.262, B:F.267, B:F.267, B:P.303 Hydrogen bonds: B:Q.265 Salt bridges: B:K.261

2 x FE: FE (III) ION(Non-functional Binders)

FE.2: 1 residues within 4Å: Ligands: 554.3 No protein-ligand interaction detected (PLIP) FE.7: 1 residues within 4Å: Ligands: 554.8 No protein-ligand interaction detected (PLIP)

2 x 554: (2~{S})-1-[(3~{S})-3-[[(3~{S})-3,4-bis(oxidanyl)-4-oxidanylidene-butyl]amino]-4-oxidanyl-4-oxidanylidene-butyl]azetidine-2-carboxylic acid(Non-covalent)

554.3: 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 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.78 Hydrogen bonds: A:G.76, A:G.133, 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.482 554.8: 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 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.78 Hydrogen bonds: B:G.76, B:G.133, 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.
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Iron-phytosiderophore transporter

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