SMTL ID : 8dto.1

Vaccine elicited Antibody MU89 bound to CH848.D949.10.17_N133D_N138T.DS.SOSIP.664 HIV-1 Env trimer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN: 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.1: 2 residues within 4Å: Chain A: N.422, T.424 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.14: 2 residues within 4Å: Chain E: N.422, T.424 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.28: 2 residues within 4Å: Chain I: N.422, T.424 No protein-ligand interaction detected (PLIP)

14 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.2: 8 residues within 4Å: Chain A: N.285, I.306 Chain D: S.23, Y.28, Y.89, A.90, G.91, S.92 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.90 NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: V.164, R.176, N.181 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.164 NAG-NAG-BMA.8: 4 residues within 4Å: Chain A: T.120, I.122, N.142, K.153 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 3 residues within 4Å: Chain A: N.260, T.262, N.263 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 4 residues within 4Å: Chain A: T.354, N.368, S.370 Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 8 residues within 4Å: Chain E: N.285, I.306 Chain H: S.23, Y.28, Y.89, G.91, S.92, S.93 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 3 residues within 4Å: Chain E: V.164, R.176, N.181 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.164 NAG-NAG-BMA.21: 4 residues within 4Å: Chain E: T.120, I.122, N.142, K.153 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 4 residues within 4Å: Chain E: T.354, N.368, S.370 Ligands: NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 2 residues within 4Å: Chain E: N.260, T.262 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 7 residues within 4Å: Chain E: N.322, N.374, G.375, T.376, S.383, N.385 Ligands: NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 9 residues within 4Å: Chain I: N.285, T.287, I.306 Chain L: S.23, Y.28, Y.89, A.90, G.91, S.92 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:A.90 NAG-NAG-BMA.35: 4 residues within 4Å: Chain I: T.120, I.122, N.142, K.153 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.38: 4 residues within 4Å: Chain I: T.354, N.368, S.370 Ligands: NAG-NAG.32 No protein-ligand interaction detected (PLIP)

6 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.3: 5 residues within 4Å: Chain A: N.138, Y.155, L.157, G.303, D.304 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.9: 9 residues within 4Å: Chain A: E.56, E.195, L.245, N.246, N.359, G.361, R.426, S.427 Ligands: NAG-NAG-NAG.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.361, A:R.426 NAG-NAG-BMA-MAN-MAN.16: 5 residues within 4Å: Chain E: N.138, Y.155, L.157, G.303, D.304 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.22: 11 residues within 4Å: Chain E: E.56, E.195, L.245, N.246, F.358, N.359, C.360, G.361, R.426, S.427 Ligands: NAG-NAG-NAG.23 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.361, E:R.426 NAG-NAG-BMA-MAN-MAN.30: 4 residues within 4Å: Chain I: N.138, Y.155, G.303, D.304 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.36: 10 residues within 4Å: Chain I: E.56, E.195, P.196, L.245, N.246, F.358, N.359, G.361, R.426 Ligands: NAG-NAG-NAG.37 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:G.361, I:R.426

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

NAG-NAG.5: 4 residues within 4Å: Chain A: Q.345, S.370, N.374 Ligands: NAG-NAG-BMA.12 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: E.75, N.213, N.225 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.75 NAG-NAG.13: 3 residues within 4Å: Chain A: K.342, N.344, R.449 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain E: Q.345, S.370, N.374 Ligands: NAG-NAG-BMA.24, NAG-NAG-BMA.27 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain E: N.213, N.225 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain E: K.342, N.344, R.449 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain I: V.164, R.176, N.181 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:V.164 NAG-NAG.32: 3 residues within 4Å: Chain I: S.370, N.374 Ligands: NAG-NAG-BMA.38 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain I: E.75, N.213, N.225 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain I: K.342, N.344, R.449 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.7: 19 residues within 4Å: Chain A: T.281, H.313, N.315, T.393, T.395 Chain C: H.32, W.101, S.103, Y.105, Y.106, N.113, D.115, Y.116 Chain D: Y.44, Y.47, E.48, K.51, P.53, A.54 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.103, C:S.103 NAG-NAG-BMA-MAN-MAN-MAN-MAN.20: 19 residues within 4Å: Chain E: T.281, H.313, N.315, T.393, T.395 Chain G: H.32, W.101, S.103, Y.105, Y.106, N.113, D.115, Y.116 Chain H: Y.44, Y.47, E.48, K.51, P.53, A.54 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.103, G:S.103 NAG-NAG-BMA-MAN-MAN-MAN-MAN.34: 20 residues within 4Å: Chain I: T.281, H.313, N.315, T.393, T.395 Chain K: H.32, W.101, S.103, Y.105, Y.106, N.113, D.115, Y.116 Chain L: Y.44, Y.47, E.48, K.51, R.52, P.53, A.54 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:S.103, K:S.103

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

NAG-NAG-NAG.10: 4 residues within 4Å: Chain A: N.246, P.275, N.428 Ligands: NAG-NAG-BMA-MAN-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.23: 4 residues within 4Å: Chain E: N.246, P.275, N.428 Ligands: NAG-NAG-BMA-MAN-MAN.22 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.37: 4 residues within 4Å: Chain I: N.246, P.275, N.428 Ligands: NAG-NAG-BMA-MAN-MAN.36 No protein-ligand interaction detected (PLIP)

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

NAG.40: 1 residues within 4Å: Chain A: N.338 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.338 NAG.41: 4 residues within 4Å: Chain A: N.218, S.258, N.260, L.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.258, A:S.258 NAG.42: 6 residues within 4Å: Chain A: N.322, Y.343, N.374, G.375, T.376, S.383 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.376, A:S.383 NAG.43: 2 residues within 4Å: Chain A: N.378, I.382 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.382 NAG.44: 1 residues within 4Å: Chain E: N.338 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.338 NAG.45: 5 residues within 4Å: Chain E: N.218, T.220, S.258, N.260, L.261 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.258, E:S.258 NAG.46: 3 residues within 4Å: Chain E: N.378, T.380, I.382 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.378, E:T.380, E:T.380 NAG.47: 1 residues within 4Å: Chain I: N.338 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.338 NAG.48: 6 residues within 4Å: Chain I: N.218, T.220, R.257, S.258, N.260, L.261 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:S.258, I:S.258 NAG.49: 3 residues within 4Å: Chain I: N.260, T.262, N.263 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:T.262 NAG.50: 6 residues within 4Å: Chain I: N.322, Y.343, N.374, G.375, T.376, S.383 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:G.375, I:T.376 NAG.51: 1 residues within 4Å: Chain I: N.378 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wiehe, K. et al., Mutation-Guided Vaccine Design: A Strategy for Developing Boosting Immunogens for HIV Broadly Neutralizing Antibody Induction. bioRxiv (2022)

Release Date

2023-04-19

Peptides

CH848.3.D0949.10.17chim.6R.DS.SOSIP.664_N133D_N138T gp120: AEI
Envelope Glycoprotein gp141: BFJ
MU89 Heavy Chain: CGK
MU89 Light Chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

E
A

I
I

B
F

F
B

J
J

C
G

G
C

K
K

D
H

H
D

L
L

CH848.3.D0949.10.17chim.6R.DS.SOSIP.664_N133D_N138T gp120

Envelope Glycoprotein gp141

MU89 Heavy Chain

MU89 Light Chain

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