SMTL ID : 8p2y.1

Structure of human SIT1:ACE2 complex (closed PD conformation)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: D.143, N.166, Y.262, N.697, S.699, D.700 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.166, A:Y.262 NAG-NAG-BMA.3: 6 residues within 4Å: Chain B: D.143, N.166, Y.262, N.697, S.699, D.700 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.166, B:Y.262

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: K.33, N.97, V.100 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: K.33, N.97, V.100 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 3 residues within 4Å: Chain A: H.381, H.385, E.409 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.381, A:H.385, A:E.409, A:E.409 ZN.11: 3 residues within 4Å: Chain B: H.381, H.385, E.409 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.381, B:H.385, B:E.409, B:E.409

2 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Post Translational Modification)

NDG.6: 3 residues within 4Å: Chain A: T.737, L.738, G.739 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.737 NDG.12: 3 residues within 4Å: Chain B: T.737, L.738, G.739 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.737

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 3 residues within 4Å: Chain A: Q.88, Q.108, N.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.88 NAG.8: 3 residues within 4Å: Chain A: E.319, V.323, N.329 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.323 Hydrogen bonds: A:N.329 NAG.9: 4 residues within 4Å: Chain A: F.292, N.439, I.443, W.601 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.292, A:I.443 NAG.10: 3 residues within 4Å: Chain A: S.427, S.552, N.553 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.427, A:S.552 NAG.13: 3 residues within 4Å: Chain B: Q.88, Q.108, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.88 NAG.14: 3 residues within 4Å: Chain B: E.319, V.323, N.329 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.323 Hydrogen bonds: B:N.329 NAG.15: 4 residues within 4Å: Chain B: F.292, N.439, I.443, W.601 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.292, B:I.443 NAG.16: 3 residues within 4Å: Chain B: S.427, S.552, N.553 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.427, B:S.552 NAG.17: 2 residues within 4Å: Chain C: N.129, N.131 No protein-ligand interaction detected (PLIP) NAG.18: 4 residues within 4Å: Chain C: F.352, I.355, K.356, N.357 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:K.356 NAG.19: 2 residues within 4Å: Chain D: N.129, N.131 No protein-ligand interaction detected (PLIP) NAG.20: 4 residues within 4Å: Chain D: F.352, I.355, K.356, N.357 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:K.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H.Z. et al., Structure and function of the SIT1 proline transporter in complex with the COVID-19 receptor ACE2. Nat Commun (2024)

Release Date

2024-06-12

Peptides

Processed angiotensin-converting enzyme 2: AB
Sodium- and chloride-dependent transporter XTRP3: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Processed angiotensin-converting enzyme 2

Sodium- and chloride-dependent transporter XTRP3

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