SMTL ID : 8ult.1

Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 04_A06 Fabs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 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: 11 residues within 4Å: Chain A: E.179, P.180, V.222, L.229, N.230, N.344, C.345, G.346, C.411, V.412, S.413 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.346 NAG-NAG-BMA.7: 9 residues within 4Å: Chain C: E.179, P.180, L.229, N.230, N.344, G.346, C.411, V.412, S.413 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.33, C:G.346 NAG-NAG-BMA.18: 9 residues within 4Å: Chain E: E.179, P.180, L.229, N.230, N.344, G.346, C.411, V.412, S.413 No protein-ligand interaction detected (PLIP)

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.2: 5 residues within 4Å: Chain A: Q.261, N.263, S.301, R.410, V.412 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain A: N.263, T.265, H.297, N.299, S.379, T.381, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: N.330, S.331, T.339, N.353, S.355 Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.353, S.355 Ligands: NAG-NAG.4, NAG-NAG.4, NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: E.243, N.244, T.246 Chain H: D.114, D.115 Chain K: D.28, W.31 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:W.31 NAG-NAG.8: 4 residues within 4Å: Chain C: Q.261, N.263, S.301, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: T.265, H.297, N.299, T.381 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain C: N.330, S.331, T.339, S.355 Ligands: NAG-NAG.11, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain C: N.353, S.355 Ligands: NAG-NAG.10, NAG-NAG.10, NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain C: N.244, T.246 Chain I: D.115 Chain L: D.28, V.29, G.30, W.31 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:W.31 NAG-NAG.13: 6 residues within 4Å: Chain E: Q.261, N.263, V.300, S.301, S.379, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain E: T.265, H.297, N.299, S.379, T.381, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain E: N.330, S.331, N.353 Ligands: NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain E: N.353, S.355 Ligands: NAG-NAG.15, NAG.48 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain E: N.230, P.259, N.414 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 7 residues within 4Å: Chain E: N.244, T.246 Chain G: D.115 Chain J: D.28, G.30, W.31, T.50 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:W.31, J:T.50 Hydrogen bonds: J:W.31

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

NAG.20: 3 residues within 4Å: Chain A: E.55, N.56 Chain B: S.17 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.101, G.112, K.115, R.138 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain A: V.102, N.104, N.116, Y.133, D.288 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain A: T.96, Q.98, S.118, F.119, N.120 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: R.160, N.165, T.166 Chain H: S.86 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.269 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: K.302, N.306, W.362 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.359 Ligands: NAG-NAG.5 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.230, P.259, N.414 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: N.202, T.204, G.205, S.242 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: E.55, N.56 Chain D: S.17 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: N.101, G.112, K.115, R.138 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain C: V.102, N.104, N.116, Y.133, D.288 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: Q.98, S.118, F.119, N.120 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: R.160, N.165 Chain E: R.276 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.269, V.408 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.306 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.359 Ligands: NAG-NAG.11 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.230, P.259, N.414 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.202, T.204 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain E: E.55, N.56 Chain F: S.17 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: N.101, K.115, R.138 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain E: V.102, N.104, N.116, Y.133, D.288 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain E: T.96, Q.98, S.118, F.119, N.120, K.131 Ligand excluded by PLIP NAG.44: 6 residues within 4Å: Chain A: R.276 Chain E: V.142, R.160, N.165 Chain G: D.84, S.86 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: N.202, T.204, S.242 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain E: N.269 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain E: K.302, N.306 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: N.359 Ligands: NAG-NAG.16 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

DeLaitsch, A.T. et al., Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 04_A06 Fabs. To Be Published

Release Date

2025-04-16

Peptides

Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF
04_A06 Fab Heavy Chain: GHI
04_A06 Fab Light Chain: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
H

H
I

I
J

J
L

K
M

L
N

Envelope glycoprotein gp120

Envelope glycoprotein gp41

04_A06 Fab Heavy Chain

04_A06 Fab Light Chain

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