SMTL ID : 7kde.1

BG505 SOSIP.664 in complex with the V3-targeting rhesus macaque antibody 1485 and human gp120-gp41 interface antibody 8ANC195

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-3-mer

Ligands

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

NAG-NAG-BMA-FUC.1: 8 residues within 4Å: Chain A: S.125, N.126 Chain N: W.108 Chain O: N.32, Y.50, R.51, A.53, A.54 No protein-ligand interaction detected (PLIP)

1 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.2: 8 residues within 4Å: Chain B: S.125, N.126 Chain J: W.108, S.109 Chain K: N.32, Y.50, R.51, A.54 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Y.50

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.3: 7 residues within 4Å: Chain C: N.126 Chain L: S.109 Chain M: N.32, Y.50, R.51, A.53, A.54 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:Y.50, M:A.53, M:L.55 NAG-NAG-BMA.6: 6 residues within 4Å: Chain D: L.229, N.230, C.345, V.412, S.413 Ligands: NAG.40 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 8 residues within 4Å: Chain D: N.244, T.246, N.247 Chain N: Q.1, H.3, Y.25, G.26, N.28 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:Q.1, N:Q.1

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.4: 6 residues within 4Å: Chain D: N.116, Y.133, L.135 Chain I: D.74, W.76, R.77 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.77, I:R.77, I:R.77 NAG-NAG-BMA-MAN.10: 7 residues within 4Å: Chain E: N.116, Y.133, L.135, D.288 Chain H: D.74, W.76, R.77 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:D.74, H:R.77

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN.5: 13 residues within 4Å: Chain D: N.202, H.319 Chain N: T.19, W.55, S.57, R.64, L.68, S.70, A.71, V.72, D.73, S.83, E.85 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:A.71, N:D.73, N:R.64, N:R.64

2 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.8: 12 residues within 4Å: Chain D: T.265, H.297, N.299, T.381 Chain I: P.101, N.102, H.103, D.108, S.109, Y.114, E.116 Chain R: R.50 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.14: 15 residues within 4Å: Chain E: T.265, H.297, N.299, T.381, R.410 Chain H: P.101, N.102, H.103, W.104, D.108, S.109, Y.114, E.116 Chain P: R.50, D.51 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:E.105, H:E.105

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

NAG-NAG.9: 2 residues within 4Å: Chain D: N.353 Ligands: NAG.38 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain E: L.229, N.230, N.344, V.412, S.413 Ligands: NAG.51 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain E: N.353, S.355 Ligands: NAG.49 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain F: N.101, G.112 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 7 residues within 4Å: Chain F: L.229, N.230, N.344, C.345, V.412, S.413 Ligands: NAG-NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain F: Q.261, N.263, V.300, S.301, R.410, V.412 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain F: N.353, S.355 Ligands: NAG.57, NAG.58 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain F: P.259, V.412, N.414 Ligands: NAG-NAG.19 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.11: 11 residues within 4Å: Chain E: N.202 Chain L: T.29, W.55, S.57, R.64, S.70, A.71, V.72, D.73, I.81, S.83 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:A.71, L:D.73, L:R.64, L:R.64 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.18: 10 residues within 4Å: Chain F: N.202 Chain J: T.29, W.55, S.57, R.64, S.70, A.71, V.72, D.73, S.83 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:A.71, J:D.73, J:S.57, J:R.64, J:R.64

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.13: 8 residues within 4Å: Chain E: N.244, T.246, N.247 Chain L: Q.1, H.3, Y.25, G.26, N.28 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Q.1 NAG-NAG-BMA-MAN-MAN.17: 4 residues within 4Å: Chain F: N.116, L.135 Chain G: D.74, R.77 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:W.76, G:R.77, G:R.77 NAG-NAG-BMA-MAN-MAN.20: 7 residues within 4Å: Chain F: N.244, T.246, N.247 Chain J: Q.1, H.3, Y.25, G.26 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:Y.25 Hydrogen bonds: J:Q.1, J:Q.1

1 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.22: 10 residues within 4Å: Chain F: H.297, N.299, T.381, R.410 Chain G: P.101, W.104, E.105, D.108, S.109, Y.114 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:E.105, G:E.105

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

NAG.25: 3 residues within 4Å: Chain A: N.107, S.109, E.110 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.100 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.107, S.109, E.110 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.100, S.102 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.107, S.109, E.110 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: S.17 Chain D: N.56 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain D: N.101 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain D: T.96, Q.98, S.118, F.119, N.120 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: R.160, N.165, T.166 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain D: Q.261, N.263, N.299, V.300, S.301, S.379 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain D: N.269, G.407 Chain I: Y.53, S.56 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain D: K.302, N.306 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain D: N.330, S.332, G.333 Ligands: NAG-NAG.9, NAG-NAG.9 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain D: S.355, N.359 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain D: V.412, N.414 Ligands: NAG-NAG-BMA.6 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: S.17 Chain E: E.55, N.56 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain E: N.101, G.112 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: Q.98, N.120, K.131 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain E: R.160, N.165, T.166 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain E: Q.261, N.263, V.300, S.301 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain E: N.269, G.407, V.408 Chain H: S.56, I.58 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain E: N.306 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain E: N.322 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain E: N.330, G.333 Ligands: NAG-NAG.15, NAG-NAG.15 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain E: G.356, N.359 Ligand excluded by PLIP NAG.51: 6 residues within 4Å: Chain E: N.230, L.233, P.259, V.412, N.414 Ligands: NAG-NAG.12 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain B: S.17 Chain F: E.55, N.56 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain F: T.96, Q.98, N.120 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain F: R.160, N.165, T.166 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain F: N.269 Chain G: Y.53, S.56, Y.106, F.107 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain F: N.306 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain F: N.330, S.331, S.355 Ligands: NAG-NAG.23, NAG-NAG.23 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain F: G.356, N.359 Ligands: NAG-NAG.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., A broadly neutralizing macaque monoclonal antibody against the HIV-1 V3-Glycan patch. Elife (2020)

Release Date

2020-10-28

Peptides

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41: ABC
Envelope glycoprotein gp120: DEF
Ab 1485 Heavy Chain: GHI
8ANC195 Fab Heavy Chain: JLN
8ANC195 Fab Light Chain: KMO
Ab 1485 Light Chain: PQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
G

G
H

H
J

I
M

J
O

L
Q

N
S

K
P

M
R

O
T

P
I

Q
L

R
N

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41

Envelope glycoprotein gp120

Ab 1485 Heavy Chain

8ANC195 Fab Heavy Chain

8ANC195 Fab Light Chain

Ab 1485 Light Chain

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