SMTL ID : 8p31.1

Structure of human SIT1:ACE2 complex (closed 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: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.166 NAG-NAG-BMA.3: 6 residues within 4Å: Chain B: D.143, N.166, Y.262, N.697, S.699, D.700 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.166

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: 1 residues within 4Å: 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.20: 1 residues within 4Å: Chain D: N.131 No protein-ligand interaction detected (PLIP) NAG.21: 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: 15 residues within 4Å: Chain C: Y.21, A.22, V.23, G.24, L.25, G.26, N.27, L.98, Y.102, F.250, S.251, G.253, F.256, S.406, N.410 9 PLIP interactions: 9 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.406 YCP.22: 15 residues within 4Å: Chain D: Y.21, A.22, V.23, G.24, L.25, G.26, N.27, L.98, Y.102, F.250, S.251, G.253, F.256, S.406, N.410 9 PLIP interactions: 9 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.406

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.
Show / Hide

Processed angiotensin-converting enzyme 2

Sodium- and chloride-dependent transporter XTRP3

Related Entries With Identical Sequence