SMTL ID : 8e5s.1

X-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter WT in an occluded state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

monomer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: D.274, D.347, P.348, S.349 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.274, A:S.349

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

OLC.3: 14 residues within 4Å: Chain A: L.61, V.65, N.68, N.72, R.232, V.235, I.243, L.383, V.384, T.385, R.386, F.389, I.396 Ligands: OLC.5 Ligand excluded by PLIP OLC.4: 6 residues within 4Å: Chain A: L.372, A.375, R.376, W.394, V.398 Ligands: OLC.12 Ligand excluded by PLIP OLC.5: 6 residues within 4Å: Chain A: R.232, R.236, R.239, R.386, F.389 Ligands: OLC.3 Ligand excluded by PLIP OLC.6: 4 residues within 4Å: Chain A: W.328, L.329, L.332, I.333 Ligand excluded by PLIP OLC.7: 9 residues within 4Å: Chain A: L.57, N.60, M.64, G.183, F.186, G.247, L.251, M.254 Ligands: OLC.13 Ligand excluded by PLIP OLC.8: 9 residues within 4Å: Chain A: I.358, F.361, F.365, I.401, N.404, G.405, L.408 Ligands: OLC.15, OLC.21 Ligand excluded by PLIP OLC.9: 8 residues within 4Å: Chain A: V.172, V.173, R.176, P.177, L.179, V.182, M.254, S.255 Ligand excluded by PLIP OLC.10: 4 residues within 4Å: Chain A: A.244, G.247, L.248, L.251 Ligand excluded by PLIP OLC.11: 5 residues within 4Å: Chain A: R.387, S.388, V.391, I.392 Ligands: OLC.16 Ligand excluded by PLIP OLC.12: 5 residues within 4Å: Chain A: R.387, V.391, W.394 Ligands: OLC.4, OLC.16 Ligand excluded by PLIP OLC.13: 3 residues within 4Å: Chain A: L.179, A.180 Ligands: OLC.7 Ligand excluded by PLIP OLC.14: 5 residues within 4Å: Chain A: W.54, L.57, A.58, L.61, F.186 Ligand excluded by PLIP OLC.15: 3 residues within 4Å: Chain A: M.346, L.354 Ligands: OLC.8 Ligand excluded by PLIP OLC.16: 3 residues within 4Å: Chain A: V.395 Ligands: OLC.11, OLC.12 Ligand excluded by PLIP OLC.17: 4 residues within 4Å: Chain A: F.129, W.130, V.133, V.134 Ligand excluded by PLIP OLC.18: 6 residues within 4Å: Chain A: V.166, L.169, V.170, V.173, L.174, L.248 Ligand excluded by PLIP OLC.19: 6 residues within 4Å: Chain A: W.95, W.98, I.99, E.102, L.103, M.106 Ligand excluded by PLIP OLC.20: 6 residues within 4Å: Chain A: L.103, M.106, L.110, V.341, V.351, L.354 Ligand excluded by PLIP OLC.21: 10 residues within 4Å: Chain A: W.89, L.93, Y.97, P.364, F.365, V.368, L.372, I.401 Ligands: OLC.8, PEG.29 Ligand excluded by PLIP OLC.22: 2 residues within 4Å: Chain A: A.289, V.292 Ligand excluded by PLIP OLC.23: 10 residues within 4Å: Chain A: I.27, L.142, T.150, L.153, E.154, V.157, L.303, S.304, A.307, V.308 Ligand excluded by PLIP OLC.24: 5 residues within 4Å: Chain A: Q.121, L.122, L.123, T.124 Ligands: PEG.27 Ligand excluded by PLIP OLC.25: 6 residues within 4Å: Chain A: V.26, S.29, I.30, M.33, L.162, A.245 Ligand excluded by PLIP OLC.26: 1 residues within 4Å: Chain A: M.163 Ligand excluded by PLIP

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.27: 2 residues within 4Å: Chain A: S.291 Ligands: OLC.24 No protein-ligand interaction detected (PLIP) PEG.28: 4 residues within 4Å: Chain A: R.86, R.91, V.94, W.95 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.91, A:V.94 Hydrogen bonds: A:R.86 PEG.29: 5 residues within 4Å: Chain A: R.88, W.89, F.373, R.376 Ligands: OLC.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.88

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.30: 2 residues within 4Å: Chain A: G.345, D.347 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.347, A:D.347 GOL.31: 3 residues within 4Å: Chain A: Y.48, G.194, Y.197 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.48, A:Y.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ray, S. et al., High-resolution structures with bound Mn 2+ and Cd 2+ map the metal import pathway in an Nramp transporter. Elife (2023)

Release Date

2023-05-03

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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