SMTL ID : 6vo3.1

AMC009 SOSIP.v4.2 in complex with PGV04 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

9 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 C: R.231, P.232, V.233, L.240, N.241, N.354, C.355, G.356, R.416, C.417, S.418 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.356, C:R.416 NAG-NAG-BMA.3: 4 residues within 4Å: Chain C: V.349, M.350, N.363, T.365 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 6 residues within 4Å: Chain A: Q.68 Chain C: A.337, F.338, N.339, Q.340, S.370 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 11 residues within 4Å: Chain G: R.231, P.232, V.233, L.240, N.241, N.354, C.355, G.356, R.416, C.417, S.418 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.356, G:R.416 NAG-NAG-BMA.10: 4 residues within 4Å: Chain G: V.349, M.350, N.363, T.365 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 6 residues within 4Å: Chain E: Q.68 Chain G: A.337, F.338, N.339, Q.340, S.370 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 11 residues within 4Å: Chain K: R.231, P.232, V.233, L.240, N.241, N.354, C.355, G.356, R.416, C.417, S.418 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:G.356, K:R.416 NAG-NAG-BMA.17: 4 residues within 4Å: Chain K: V.349, M.350, N.363, T.365 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 6 residues within 4Å: Chain I: Q.68 Chain K: A.337, F.338, N.339, Q.340, S.370 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: 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.2: 9 residues within 4Å: Chain B: Y.28, G.29, H.30, Q.64, F.65, G.66 Chain C: N.255, F.256, T.257 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.29 NAG-NAG-BMA-MAN-MAN.9: 9 residues within 4Å: Chain F: Y.28, G.29, H.30, Q.64, F.65, G.66 Chain G: N.255, F.256, T.257 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.29 NAG-NAG-BMA-MAN-MAN.16: 9 residues within 4Å: Chain J: Y.28, G.29, H.30, Q.64, F.65, G.66 Chain K: N.255, F.256, T.257 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:G.29

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

NAG-NAG.4: 4 residues within 4Å: Chain C: Q.340, T.365, Q.366, N.369 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: E.55, N.208, N.220 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: E.59, N.60 Chain D: G.17, S.18 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain G: Q.340, T.365, Q.366, N.369 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain G: E.55, N.208, N.220 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain G: E.59, N.60 Chain H: G.17, S.18 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain K: Q.340, T.365, Q.366, N.369 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain K: E.55, N.208, N.220 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain K: E.59, N.60 Chain L: G.17, S.18 No protein-ligand interaction detected (PLIP)

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

NAG.22: 2 residues within 4Å: Chain C: N.373, D.374 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: V.272, S.418, S.419, N.420 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.435, K.436 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: K.211, F.212, N.213, T.215 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain C: V.159, R.171, L.172, N.176 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain D: N.115 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain G: N.373, D.374 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain G: V.272, S.418, S.419, N.420 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain G: N.435, K.436 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain G: K.211, F.212, N.213, T.215 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain G: V.159, R.171, L.172, N.176 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain H: N.115 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain K: N.373, D.374 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain K: V.272, S.418, S.419, N.420 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain K: N.435, K.436 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain K: K.211, F.212, N.213, T.215 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain K: V.159, R.171, L.172, N.176 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain L: N.115 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schorcht, A. et al., Neutralizing Antibody Responses Induced by HIV-1 Envelope Glycoprotein SOSIP Trimers Derived from Elite Neutralizers. J.Virol. (2020)

Release Date

2020-09-23

Peptides

PGV04 heavy chain: AEI
PGV04 light chain: BFJ
AMC009 SOSIP.v4.2 envelope glycoprotein gp120: CGK
AMC009 SOSIP.v4.2 envelope glycoprotein gp41: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

E
G

I
I

B
L

F
J

J
K

C
A

G
C

K
D

D
B

H
E

L
F

PGV04 heavy chain

PGV04 light chain

AMC009 SOSIP.v4.2 envelope glycoprotein gp120

AMC009 SOSIP.v4.2 envelope glycoprotein gp41

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