SMTL ID : 8czj.1

A bacteria Zrt/Irt-like protein in the apo state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: H.22, P.23, L.24, I.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.24, A:I.25 Salt bridges: A:H.22 SO4.2: 4 residues within 4Å: Chain A: H.286, E.287, T.288, T.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.289 Salt bridges: A:H.286 SO4.3: 4 residues within 4Å: Chain A: S.84, A.85, R.86, H.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.85, A:R.86 Salt bridges: A:H.286 SO4.6: 7 residues within 4Å: Chain A: P.225, I.226, G.227, R.228 Chain B: S.6, L.7, A.8 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:L.7, B:A.8, A:G.227, A:R.228 Salt bridges: A:R.228 SO4.8: 6 residues within 4Å: Chain A: S.6, L.7, A.8 Chain B: P.225, G.227, R.228 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.227, B:R.228, A:L.7, A:A.8 Salt bridges: B:R.228 SO4.9: 3 residues within 4Å: Chain B: H.286, T.288, T.289 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.288, B:T.289 Salt bridges: B:H.286 SO4.10: 8 residues within 4Å: Chain A: V.54, H.55, V.56 Chain B: V.54, H.55, V.56, G.57 Ligands: MPG.7 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.56, B:V.56, B:G.57 Salt bridges: A:H.55 SO4.11: 4 residues within 4Å: Chain B: S.84, A.85, R.86, H.286 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.85, B:R.86 Salt bridges: B:H.286

9 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)

MPG.4: 9 residues within 4Å: Chain A: W.15, A.19, L.143, F.146, T.147, L.176, H.177, P.180 Ligands: MPG.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.15, A:W.15, A:L.143, A:F.146, A:T.147, A:L.176, A:H.177, A:P.180 MPG.5: 7 residues within 4Å: Chain A: T.26, L.29, A.30, A.33, L.179, M.183 Ligands: MPG.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.26, A:L.29, A:L.29, A:A.30, A:A.33, A:L.179 MPG.7: 15 residues within 4Å: Chain A: I.44, A.47, N.52, R.53, V.54, M.239, L.242, L.245, V.246, G.249 Chain B: G.57, V.60, L.61 Ligands: SO4.10, MPG.14 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.44, A:A.47, A:L.242, A:L.245, A:V.246 Hydrogen bonds: A:R.53, A:V.54 MPG.12: 17 residues within 4Å: Chain A: G.57, Y.58, V.60, L.61, L.238 Chain B: L.40, A.47, N.52, R.53, V.54, V.56, L.179, M.239, L.242, L.245, V.246, G.249 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.40, B:A.47, B:L.179, B:L.242, B:L.245, B:V.246, A:V.60, A:L.61, A:L.238 Hydrogen bonds: B:N.52, B:R.53, B:V.54, B:V.54 MPG.13: 6 residues within 4Å: Chain B: T.26, L.29, A.33, L.179, M.183 Ligands: MPG.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.29, B:A.33, B:L.179 MPG.14: 12 residues within 4Å: Chain A: L.40, A.47, L.48, G.50 Chain B: Y.58, L.61, G.62, A.64, A.65, L.194, L.198 Ligands: MPG.7 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.61, B:A.64, B:A.65, B:L.194, B:L.198, A:L.40 Hydrogen bonds: B:Y.58, A:G.50 MPG.15: 6 residues within 4Å: Chain B: G.134, V.137, L.138, L.141, Y.145, H.275 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.137, B:L.138, B:L.141 MPG.16: 7 residues within 4Å: Chain B: L.24, L.27, G.28, A.31, L.138 Ligands: MPG.13, MPG.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.24, B:L.27, B:A.31, B:L.138 MPG.17: 3 residues within 4Å: Chain B: P.23, L.27 Ligands: MPG.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Structural insights into the elevator-type transport mechanism of a bacterial ZIP metal transporter. Nat Commun (2023)

Release Date

2023-02-22

Peptides

Putative membrane protein: 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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Putative membrane protein

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