SMTL ID : 8p30.1

Structure of human SIT1:ACE2 complex (open PD conformation) bound to L-pipecolate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 12 residues within 4Å: Chain A: N.141, P.142, D.143, D.164, N.166, E.167, L.169, W.170, E.173, N.697, S.699, D.700 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.169 NAG-NAG-BMA-MAN-MAN-MAN-MAN.3: 12 residues within 4Å: Chain B: N.141, P.142, D.143, D.164, N.166, E.167, L.169, W.170, E.173, N.697, S.699, D.700 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.169

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: 2 residues within 4Å: Chain A: N.97, V.100 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: 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: 2 residues within 4Å: Chain A: E.319, N.329 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain A: F.292, N.439, E.440 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.292, A:E.440 NAG.10: 4 residues within 4Å: Chain A: S.427, D.550, 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: 2 residues within 4Å: Chain B: E.319, N.329 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain B: F.292, N.439, E.440 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.292, B:E.440 NAG.16: 4 residues within 4Å: Chain B: S.427, D.550, 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 A: Q.735 Chain C: N.131 No protein-ligand interaction detected (PLIP) NAG.18: 4 residues within 4Å: Chain C: F.352, P.353, I.355, N.357 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain B: Q.735 Chain D: N.131 No protein-ligand interaction detected (PLIP) NAG.22: 4 residues within 4Å: Chain D: F.352, P.353, I.355, N.357 No protein-ligand interaction detected (PLIP)

2 x YCP: (2S)-piperidine-2-carboxylic acid(Non-covalent)

YCP.19: 14 residues within 4Å: Chain C: Y.21, A.22, G.24, L.25, G.26, N.27, L.98, Y.102, F.250, S.251, G.253, F.256, S.406, N.410 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.98, C:Y.102, C:F.250, C:F.256 Hydrogen bonds: C:G.24, C:G.26, C:Y.102, C:F.250, C:S.251, C:S.406 YCP.23: 14 residues within 4Å: Chain D: Y.21, A.22, G.24, L.25, G.26, N.27, L.98, Y.102, F.250, S.251, G.253, F.256, S.406, N.410 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.98, D:Y.102, D:F.250, D:F.256 Hydrogen bonds: D:G.24, D:G.26, D:Y.102, D:F.250, D:S.251, D:S.406

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

CL.20: 6 residues within 4Å: Chain C: N.27, Y.47, Q.247, S.251, N.283, S.287 Ligand excluded by PLIP CL.24: 6 residues within 4Å: Chain D: N.27, Y.47, Q.247, S.251, N.283, S.287 Ligand excluded by PLIP

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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