SMTL ID : 5x5p.1

Human serum transferrin bound to ruthenium NTA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 10 residues within 4Å: Chain A: D.392, Y.426, T.452, R.456, T.457, A.458, G.459, Y.517, H.585 Ligands: FE.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.456, A:Y.517 Hydrogen bonds: A:T.457, A:A.458, A:G.459 Salt bridges: A:R.456, A:H.585

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

FE.2: 5 residues within 4Å: Chain A: D.392, Y.426, Y.517, H.585 Ligands: MLI.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.392, A:Y.426, A:Y.517, A:H.585

4 x RU: RUTHENIUM ION(Non-covalent)

RU.3: 2 residues within 4Å: Chain A: H.14 Ligands: NTA.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.14, H2O.1 RU.4: 2 residues within 4Å: Chain A: H.578 Ligands: NTA.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.578, NTA.8 RU.5: 1 residues within 4Å: Chain A: H.273 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.273, H2O.1, H2O.1 RU.6: 1 residues within 4Å: Chain A: H.289 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.289

2 x NTA: NITRILOTRIACETIC ACID(Non-covalent)

NTA.7: 3 residues within 4Å: Chain A: H.14, H.289 Ligands: RU.3 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:H.14, A:H.14, A:H.14, A:H.289 NTA.8: 4 residues within 4Å: Chain A: H.578, A.580, R.581 Ligands: RU.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.581 Salt bridges: A:H.578, A:H.578, A:H.578, A:R.581

1 x NA: SODIUM ION(Non-functional Binders)

NA.9: 4 residues within 4Å: Chain A: S.125, N.129, Y.319, I.323 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, M. et al., Binding of ruthenium and osmium at non‐iron sites of transferrin accounts for their iron-independent cellular uptake. J.Inorg.Biochem. (2022)

Release Date

2018-02-21

Peptides

Serotransferrin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Serotransferrin

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