SMTL ID : 6vkn.1

BG505 SOSIP.v5.2.N241.N289 in complex with rhesus macaque Fab RM19R

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

18 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: E.57, N.58 Chain B: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: K.199, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.246, N.249 Ligands: NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.118, Y.135, L.137 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.135 Hydrogen bonds: A:Y.135 NAG-NAG.8: 2 residues within 4Å: Chain B: N.126, Y.127 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain E: E.57, N.58 Chain F: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain E: K.199, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain E: N.246, N.249 Ligands: NAG.38 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG.39 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain E: N.118, Y.135, L.137 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.135 Hydrogen bonds: E:Y.135 NAG-NAG.16: 2 residues within 4Å: Chain F: N.126, Y.127 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain I: E.57, N.58 Chain J: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain I: K.199, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain I: N.246, N.249 Ligands: NAG.51 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain I: N.355, S.357 Ligands: NAG.52 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain I: N.118, Y.135, L.137 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:Y.135 Hydrogen bonds: I:Y.135 NAG-NAG.24: 2 residues within 4Å: Chain J: N.126, Y.127 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.5: 9 residues within 4Å: Chain A: E.181, P.182, V.224, L.231, N.232, G.348, V.414, S.415 Ligands: NAG.30 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.414 Hydrogen bonds: A:G.348, A:V.414 NAG-NAG-BMA-MAN-MAN-MAN.13: 9 residues within 4Å: Chain E: E.181, P.182, V.224, L.231, N.232, G.348, V.414, S.415 Ligands: NAG.43 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.414 Hydrogen bonds: E:G.348, E:V.414 NAG-NAG-BMA-MAN-MAN-MAN.21: 9 residues within 4Å: Chain I: E.181, P.182, V.224, L.231, N.232, G.348, V.414, S.415 Ligands: NAG.56 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:V.414 Hydrogen bonds: I:G.348, I:V.414

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.7: 4 residues within 4Å: Chain B: N.100, S.102, Y.127, I.130 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.127 NAG-NAG-FUC.15: 4 residues within 4Å: Chain F: N.100, S.102, Y.127, I.130 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.127 NAG-NAG-FUC.23: 4 residues within 4Å: Chain J: N.100, S.102, Y.127, I.130 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:Y.127

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

NAG.25: 4 residues within 4Å: Chain A: N.204, E.245, N.246 Ligands: NAG-NAG.3 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG-NAG.4 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.308, T.363 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain A: N.265, T.267, H.299, N.301, T.383, R.412 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.5 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: N.271, I.292, G.409, V.410 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: R.162, N.167, T.168 Chain I: R.278 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.103 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain A: E.238, E.239, N.259, E.260 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: N.107, E.110 Chain C: T.56 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain E: N.204, E.245, N.246 Ligands: NAG-NAG.11 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain E: S.357, N.361 Ligands: NAG-NAG.12 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain E: N.308, T.363 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain E: N.265, T.267, H.299, N.301, T.383, R.412 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain E: Q.263, N.265, N.301, S.303 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain E: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.13 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain E: N.271, I.292, G.409, V.410 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain A: R.278 Chain E: R.162, N.167, T.168 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain E: N.103 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain E: E.238, E.239, N.259, E.260 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain F: N.107, E.110 Chain G: T.56 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain I: N.204, E.245, N.246 Ligands: NAG-NAG.19 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain I: S.357, N.361 Ligands: NAG-NAG.20 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain I: N.308, T.363 Ligand excluded by PLIP NAG.54: 6 residues within 4Å: Chain I: N.265, T.267, H.299, N.301, T.383, R.412 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain I: Q.263, N.265, N.301, S.303 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain I: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.21 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain I: N.271, I.292, G.409, V.410 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain I: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain E: R.278 Chain I: R.162, N.167, T.168 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain I: N.103 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain I: N.324 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain I: E.238, E.239, N.259, E.260 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain J: N.107, E.110 Chain K: T.56 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martin, J.T. et al., Targeting HIV Env immunogens to B cell follicles in nonhuman primates through immune complex or protein nanoparticle formulations. NPJ Vaccines (2020)

Release Date

2020-08-12

Peptides

Envelope glycoprotein gp160: AEI
BG505 SOSIPv5.2 gp41: BFJ
RM19R Kappa Light Chain: CGK
RM19R Heavy Chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

I
D

B
B

F
E

J
F

C
L

G
J

K
K

D
H

H
G

L
I

Envelope glycoprotein gp160

BG505 SOSIPv5.2 gp41

RM19R Kappa Light Chain

RM19R Heavy Chain

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