SMTL ID : 8fyi.1

Structure of HIV-1 BG505 SOSIP-HT1 in complex with one CD4 molecule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-3-1-mer

Ligands

5 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: 4 residues within 4Å: Chain A: N.104, N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain B: V.102, N.104, N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.353, S.355 Ligands: NAG.32, NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain C: V.102, N.104, N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.353, S.355 Ligands: NAG.42, NAG.43 No protein-ligand interaction detected (PLIP)

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

NAG-BMA.2: 4 residues within 4Å: Chain A: R.410, C.411 Ligands: NAG.15, NAG.16 No protein-ligand interaction detected (PLIP) NAG-BMA.5: 4 residues within 4Å: Chain B: G.346, R.410 Ligands: NAG.27, NAG.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.33, B:K.33

1 x NAG- NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(6-8)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-NAG.3: 6 residues within 4Å: Chain A: N.330, S.331, T.339, N.353, S.355 Ligands: NAG.20 No protein-ligand interaction detected (PLIP)

1 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.8: 11 residues within 4Å: Chain C: E.179, P.180, V.222, L.229, N.230, C.345, G.346, C.411, V.412, S.413 Ligands: NAG.44 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.412 Hydrogen bonds: C:V.412

35 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.10: 4 residues within 4Å: Chain A: E.55, N.56 Chain D: G.9, S.10 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.101 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: Q.98, S.118, N.120 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: R.160, N.165 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.202, T.204, S.242, H.319 Ligand excluded by PLIP NAG.15: 10 residues within 4Å: Chain A: P.180, L.229, N.230, N.344, C.411, V.412, S.413 Ligands: NAG-BMA.2, NAG.16, NAG.21 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: E.179 Ligands: NAG-BMA.2, NAG-BMA.2, NAG.15 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.244, T.246, N.247 Chain G: K.90 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: Q.261, N.263, N.299, V.300, S.301 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.269 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: S.355, N.359 Ligands: NAG-NAG-NAG-NAG.3, NAG-NAG-NAG-NAG.3 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: V.412, N.414 Ligands: NAG.15 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: E.55, N.56 Chain E: G.9, S.10 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.101, G.112 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: Q.98, S.118, N.120, K.131 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: R.160, N.165, T.166 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.202, T.204, S.242 Ligand excluded by PLIP NAG.27: 12 residues within 4Å: Chain B: P.180, V.222, L.229, N.230, N.344, C.345, C.411, V.412, S.413 Ligands: NAG-BMA.5, NAG.28, NAG.34 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: E.179, V.412 Ligands: NAG-BMA.5, NAG-BMA.5, NAG.27 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.244, T.246 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: Q.261, N.263, S.301 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.269, I.290 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain B: N.330, S.331, T.339, S.355 Ligands: NAG-NAG.6, NAG-NAG.6 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain B: S.355, G.356, N.359 Ligands: NAG-NAG.6, NAG-NAG.6 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain B: K.220, N.230, L.233, P.259, N.414 Ligands: NAG.27 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.101 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: Q.98, S.118, N.120, K.131 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: R.276 Chain C: R.160, N.165, T.166 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: N.202, T.204, S.242, E.243 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.244, T.246, N.247 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: Q.261, N.263, S.301 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.269, I.290, V.408 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain C: N.330, S.331, T.339, S.355 Ligands: NAG-NAG.9, NAG-NAG.9 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.359 Ligands: NAG-NAG.9 Ligand excluded by PLIP NAG.44: 6 residues within 4Å: Chain C: N.230, L.233, P.259, V.412, N.414 Ligands: NAG-NAG-BMA.8 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dam, K.A. et al., Intermediate conformations of CD4-bound HIV-1 Env heterotrimers. Nature (2023)

Release Date

2023-10-18

Peptides

Envelope glycoprotein gp160: A
Envelope glycoprotein gp160: BC
Envelope glycoprotein gp41: DEF
T-cell surface glycoprotein CD4: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
Z

Envelope glycoprotein gp160

Envelope glycoprotein gp160

Envelope glycoprotein gp41

T-cell surface glycoprotein CD4

Related Entries With Identical Sequence