SMTL ID : 7y75.1

SIT1-ACE2-BA.2 RBD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: F.373, I.376, N.378 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain B: N.62, T.64, E.66, N.67, Q.349 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: K.35, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: Q.90, N.112 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: F.294, N.441, W.603 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: S.429, D.552, S.554, N.555 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: D.145, N.168, N.699, S.701, D.702 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: D.40, N.44, F.72 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain D: F.373, I.376, N.378 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain E: N.62, T.64, E.66, N.67, Q.349 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain E: K.35, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain E: Q.90, N.112 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain E: F.294, N.441, W.603 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain E: S.429, D.552, S.554, N.555 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain E: D.145, N.168, N.699, S.701, D.702 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain F: D.40, N.44, F.72 No protein-ligand interaction detected (PLIP)

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

NAG.17: 1 residues within 4Å: Chain A: N.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.152 NAG.18: 3 residues within 4Å: Chain A: F.348, T.350, N.353 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.350 Hydrogen bonds: A:N.353 NAG.22: 1 residues within 4Å: Chain B: N.331 No protein-ligand interaction detected (PLIP) NAG.24: 1 residues within 4Å: Chain D: N.152 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.152 NAG.25: 3 residues within 4Å: Chain D: F.348, T.350, N.353 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:T.350 Hydrogen bonds: D:N.353 NAG.29: 1 residues within 4Å: Chain E: N.331 No protein-ligand interaction detected (PLIP)

6 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.19: 5 residues within 4Å: Chain A: S.106, V.110, V.113, S.442, I.444 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.110, A:V.113, A:I.444 3PH.20: 3 residues within 4Å: Chain A: L.302, S.523, Y.525 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.302 Hydrogen bonds: A:S.523 3PH.21: 6 residues within 4Å: Chain A: L.200, Y.203, H.448, L.449, L.460 Chain B: I.774 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.200, A:Y.203, A:Y.203, A:H.448, A:L.449, B:I.774 3PH.26: 6 residues within 4Å: Chain D: S.106, V.110, V.113, V.114, S.442, I.444 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.110, D:V.113, D:V.114, D:I.444 3PH.27: 3 residues within 4Å: Chain D: L.302, S.523, Y.525 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.302 Hydrogen bonds: D:S.523 3PH.28: 6 residues within 4Å: Chain D: L.200, Y.203, L.449, G.456, L.460 Chain E: I.774 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:L.200, D:Y.203, D:Y.203, D:L.449, D:L.460, E:I.774

2 x ZN: ZINC ION(Non-covalent)

ZN.23: 3 residues within 4Å: Chain B: H.383, H.387, E.411 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.383, B:H.387, B:E.411, B:E.411 ZN.30: 3 residues within 4Å: Chain E: H.383, H.387, E.411 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.383, E:H.387, E:E.411, E:E.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, Y. et al., Structures of ACE2-SIT1 recognized by Omicron variants of SARS-CoV-2. Cell Discov (2022)

Release Date

2022-11-30

Peptides

Sodium- and chloride-dependent transporter XTRP3: AD
Angiotensin-converting enzyme 2: BE
Spike protein S1: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
D

B
A

E
C

C
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Sodium- and chloride-dependent transporter XTRP3

Angiotensin-converting enzyme 2

Spike protein S1

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