SMTL ID : 4rdr.1

Structure of the bacterial Zn-transporter ZnuD from Neisseria meningitidis (locked conformation bound to zinc and cadmium ions)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

monomer

Ligands

2 x CD: CADMIUM ION(Non-covalent)

CD.1: 2 residues within 4Å: Chain A: H.263, D.265 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.263, A:D.265, A:D.265 CD.2: 4 residues within 4Å: Chain A: H.255, H.257, D.260, E.361 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.257, A:D.260, A:D.260, A:E.361, A:E.361

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: S.111, D.113, H.114, E.354, H.513 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.113, A:H.114, A:E.354, A:H.513

5 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.4: 10 residues within 4Å: Chain A: T.179, L.198, Y.199, Q.224, T.225, G.226, D.245, R.247, R.321 Ligands: GOL.31 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.199 Hydrogen bonds: A:Q.224, A:R.247 C8E.5: 7 residues within 4Å: Chain A: I.599, G.613, D.614, Y.615, A.652, L.654, F.676 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.599 C8E.6: 9 residues within 4Å: Chain A: F.432, L.434, L.479, G.481, W.483, L.491, L.493, A.495 Ligands: C8E.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.483, A:W.483, A:L.491, A:L.493 C8E.7: 2 residues within 4Å: Chain A: L.175, K.177 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.177 C8E.8: 7 residues within 4Å: Chain A: F.477, L.479, N.532, N.533, R.553 Ligands: C8E.6, EDO.38 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.477, A:L.479 Hydrogen bonds: A:N.532, A:R.553

21 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 4 residues within 4Å: Chain A: R.674, F.676, A.677, R.687 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: R.617, K.680 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: G.468, A.469, R.471 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain A: K.442, K.444, R.471 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: Q.472, N.527, K.528 Ligands: GOL.30 Ligand excluded by PLIP SO4.14: 7 residues within 4Å: Chain A: Y.615, V.616, R.617, P.650, A.651, A.652, Q.678 Ligand excluded by PLIP SO4.15: 7 residues within 4Å: Chain A: Y.561, A.562, Q.563, T.564, Q.644, R.683, Y.684 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain A: T.564, R.648 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: Y.419, V.440, K.442 Ligand excluded by PLIP SO4.18: 1 residues within 4Å: Chain A: Y.199 Ligand excluded by PLIP SO4.19: 7 residues within 4Å: Chain A: T.91, G.92, A.108, D.109, F.110, S.111, P.112 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain A: R.35, H.42, R.376, K.384 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain A: T.286, P.465, D.466, K.524 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain A: R.555, D.591 Ligand excluded by PLIP SO4.23: 7 residues within 4Å: Chain A: K.602, P.605, R.606, R.608, K.659, A.660, S.661 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain A: D.567, I.574, E.575, D.577 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain A: R.544, F.601, K.602, P.603 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain A: Y.540, Y.547 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain A: D.68, H.74, A.75, A.725 Ligands: SO4.28 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain A: D.68, R.653, H.691, M.693 Ligands: SO4.27 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain A: L.399, D.413 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.30: 4 residues within 4Å: Chain A: T.473, R.475, K.528 Ligands: SO4.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.473, A:R.475, A:R.475, A:K.528 GOL.31: 3 residues within 4Å: Chain A: R.321, K.323 Ligands: C8E.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.321, A:R.321, A:K.323 GOL.32: 1 residues within 4Å: Chain A: N.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.212 GOL.33: 3 residues within 4Å: Chain A: R.674, G.690, H.692 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.674, A:G.690

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.34: 7 residues within 4Å: Chain A: R.57, L.168, R.169, L.178, S.180, Y.712, N.745 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.121, A:L.168, A:S.180, A:N.745 EDO.35: 7 residues within 4Å: Chain A: Q.77, Y.78, G.79, Y.205, T.733, P.734, Q.735 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.79, A:P.734 EDO.36: 6 residues within 4Å: Chain A: N.99, M.117, D.119, T.225, S.244, N.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.322 EDO.37: 5 residues within 4Å: Chain A: D.319, L.320, R.321, R.351, D.353 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.319, A:D.353 EDO.38: 4 residues within 4Å: Chain A: H.497, R.530, N.532 Ligands: C8E.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.530, A:N.532, A:N.532

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calmettes, C. et al., The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD. Nat Commun (2015)

Release Date

2015-08-19

Peptides

ZnuD: 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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ZnuD

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