SMTL ID : 6bu5.1

Crystal structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter in the outward-open, manganese-bound conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: A.29, Y.30, D.32, N.35, M.206 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.29, A:D.32, A:D.32, H2O.1, H2O.2 MN.2: 1 residues within 4Å: Chain A: H.263 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.263, H2O.2

1 x SPD: SPERMIDINE(Non-covalent)

SPD.3: 4 residues within 4Å: Chain A: E.41, W.199, G.271, S.347 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.41, A:W.199

10 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)(Non-functional Binders)

OLC.4: 7 residues within 4Å: Chain A: R.385, T.388, V.389, W.392, V.396 Ligands: OLC.10, OLC.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.389, A:W.392, A:W.392, A:V.396 OLC.5: 5 residues within 4Å: Chain A: L.120, L.121, Y.277, V.290 Ligands: OLC.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.290, A:V.290 Hydrogen bonds: A:Y.277 OLC.6: 5 residues within 4Å: Chain A: L.20, G.21, E.152, L.153, G.156 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.20, A:E.152, A:L.153 OLC.7: 3 residues within 4Å: Chain A: V.135, F.138, W.139 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.135, A:F.138, A:W.139, A:W.139 OLC.8: 6 residues within 4Å: Chain A: A.157, F.158, M.161, L.297, A.298 Ligands: OLC.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.157, A:F.158, A:M.161, A:L.297, A:A.298 OLC.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OLC.10: 4 residues within 4Å: Chain A: L.370, A.373, W.392 Ligands: OLC.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.392, A:W.392 OLC.11: 4 residues within 4Å: Chain A: R.385, S.386, V.389 Ligands: OLC.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.386 OLC.12: 2 residues within 4Å: Chain A: M.333, F.337 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.337, A:F.337, A:F.337 OLC.13: 3 residues within 4Å: Chain A: R.385 Ligands: OLC.4, OLC.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bozzi, A.T. et al., Structures in multiple conformations reveal distinct transition metal and proton pathways in an Nramp transporter. Elife (2019)

Release Date

2018-12-12

Peptides

Divalent metal cation transporter MntH: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Divalent metal cation transporter MntH

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