SMTL ID : 8xn1.1

Cryo-EM structure of human ZnT3, in the presence of zinc, determined in an inward-facing conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.59, D.63, H.189, D.193 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.59, A:D.63, A:D.63, A:H.189, A:D.193 ZN.2: 4 residues within 4Å: Chain A: H.270, H.287, E.321 Chain B: C.6 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.6, A:H.270, A:H.287 ZN.3: 4 residues within 4Å: Chain A: H.5, H.7 Chain B: C.330, C.333 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.5, A:H.7, B:C.330, B:C.333 ZN.7: 4 residues within 4Å: Chain A: C.330, C.333 Chain B: H.5, H.7 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.5, B:H.7, B:H.7, A:C.330, A:C.333 ZN.8: 4 residues within 4Å: Chain B: H.59, D.63, H.189, D.193 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.59, B:D.63, B:H.189, B:D.193, B:D.193 ZN.9: 4 residues within 4Å: Chain A: C.6 Chain B: H.270, H.287, E.321 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.270, B:H.287, B:E.321, B:E.321, A:C.6

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 12 residues within 4Å: Chain A: G.65, F.72, L.76, M.85, W.89, S.92, L.95, G.96, A.99 Chain B: L.240, R.241, D.341 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.240, A:F.72, A:F.72, A:L.76, A:L.95, A:A.99 Hydrogen bonds: B:D.341 Salt bridges: B:R.241 Y01.5: 11 residues within 4Å: Chain A: L.240, R.241, M.244, D.341 Chain B: M.68, F.72, L.76, M.85, W.89, G.96, A.99 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.240, B:M.68, B:L.76, B:W.89, B:A.99 Hydrogen bonds: A:D.341 Salt bridges: A:R.241

2 x AV0: Lauryl Maltose Neopentyl Glycol(Non-covalent)

AV0.6: 14 residues within 4Å: Chain A: Q.26, A.29, A.30, C.34, D.63, M.67, S.70, E.93, M.145, L.149, S.182, A.185, V.188, H.189 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Q.26, A:A.29, A:L.149 Hydrogen bonds: A:S.70, A:E.93, A:V.188, A:H.189 Salt bridges: A:H.189 AV0.11: 11 residues within 4Å: Chain B: A.30, V.33, C.34, M.67, S.70, L.149, S.182, A.185, A.186, V.188, H.189 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.30, B:V.33 Hydrogen bonds: B:S.70, B:S.70, B:E.93, B:E.93 Salt bridges: B:H.189

1 x 01: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

01.10: 7 residues within 4Å: Chain A: I.110 Chain B: W.105, Y.113, A.233, P.234, L.236, R.237 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.105, B:Y.113, B:Y.113, A:I.110 Hydrogen bonds: B:R.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Long, Y. et al., Structural insights into human zinc transporter ZnT1 mediated Zn 2+ efflux. Embo Rep. (2024)

Release Date

2024-10-30

Peptides

Probable proton-coupled zinc antiporter SLC30A3: 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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Probable proton-coupled zinc antiporter SLC30A3