SMTL ID : 7mxe.1

Ab1245 Fab in complex with BG505 SOSIP.664 and 8ANC195 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-1-1-mer

Ligands

21 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: 6 residues within 4Å: Chain C: S.125, N.126 Chain K: Y.50, R.51, A.53, A.54 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:Y.50, K:Y.50 NAG-NAG.2: 6 residues within 4Å: Chain D: N.126 Chain I: Y.50, R.51, A.53, A.54, L.55 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:Y.50, I:Y.50, I:A.53, I:L.55 NAG-NAG.3: 6 residues within 4Å: Chain A: W.108, S.109 Chain B: Y.50, A.54 Chain E: S.125, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain F: N.101, G.112 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain F: V.102, N.116, Y.133, D.288 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.133 NAG-NAG.6: 5 residues within 4Å: Chain F: Q.98, S.118, F.119, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain F: R.160, N.165, T.166 Chain H: R.276 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain F: T.265, H.297, N.299, T.381, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain H: N.104, N.116, Y.133 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain H: Q.98, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain H: R.160, N.165, T.166 Chain L: R.276 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain H: Q.261, N.263, R.410 Ligands: NAG-NAG.19 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain H: N.353, S.355 Ligands: NAG-NAG.17, NAG-NAG.18, NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain H: S.355, N.359 Ligands: NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain H: N.330, S.331, T.339 Ligands: NAG-NAG.16, NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain H: T.265, H.297, N.299, T.381, R.410 Ligands: NAG-NAG.15 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain L: V.102, N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain L: Q.98, S.118, F.119, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain L: Q.261, N.263, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain L: N.230, P.259, N.414 Ligands: NAG-NAG-BMA.29 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain L: N.353, S.355 Ligands: NAG.53, NAG.54 No protein-ligand interaction detected (PLIP)

1 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.9: 9 residues within 4Å: Chain F: K.33, E.179, N.230, N.344, C.345, G.346, V.412, S.413 Ligands: NAG.42 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.346

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.10: 7 residues within 4Å: Chain F: N.244, T.246, N.247 Chain G: Q.1, H.3, Y.25, G.26 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.1

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN.11: 17 residues within 4Å: Chain F: N.202 Chain G: T.19, T.29, W.55, S.57, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.83, E.85 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.70, G:G.65, G:I.69

2 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.20: 8 residues within 4Å: Chain A: Q.1, H.3, Y.25, G.26, N.28 Chain H: N.244, T.246, N.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.1, A:H.3 NAG-NAG-BMA-MAN-MAN.31: 9 residues within 4Å: Chain J: Q.1, H.3, V.5, Y.25, G.26, N.28 Chain L: N.244, T.246, N.247 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:Q.1, J:H.3

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.21: 20 residues within 4Å: Chain A: T.19, W.55, S.57, A.59, F.63, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.83, E.85 Chain H: K.200, N.202, H.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.73 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.30: 17 residues within 4Å: Chain J: T.19, W.55, S.57, A.59, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.83, E.85 Chain L: N.202 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:W.55 Hydrogen bonds: J:D.73

4 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.22: 6 residues within 4Å: Chain H: P.180, V.222, L.229, N.230, V.412 Ligands: NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 6 residues within 4Å: Chain H: P.259, Q.261, V.412, N.414 Chain M: S.95 Ligands: NAG-NAG-BMA.22 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 5 residues within 4Å: Chain L: T.265, H.297, N.299, T.381, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 6 residues within 4Å: Chain L: E.179, N.230, N.344, G.346, V.412 Ligands: NAG-NAG.27 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:G.346

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

NAG.33: 2 residues within 4Å: Chain C: P.98, N.100 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain E: N.100 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain D: S.17 Chain F: E.55, N.56 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain F: Q.261, N.263, N.299, S.301 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain F: N.306, W.362 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain F: N.322 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain F: N.353, S.355 Ligands: NAG.40, NAG.41 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain F: N.359 Ligands: NAG.39 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain F: N.330, S.331, N.353, S.355 Ligands: NAG.39 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain F: N.230, P.259, N.414 Ligands: NAG-NAG-BMA-MAN.9 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain F: N.269, I.290, Q.406 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain H: N.101, R.111, G.112 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain H: N.269, I.290, V.408 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain H: N.306, W.362 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain H: N.322 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: N.114 Chain H: N.56 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: S.17 Chain L: E.55, N.56 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain L: N.101, R.111, G.112 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain F: R.276 Chain L: R.160, N.165 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain L: N.322 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain L: N.359 Ligands: NAG-NAG.32 Ligand excluded by PLIP NAG.54: 6 residues within 4Å: Chain L: N.330, S.331, N.353, S.355 Ligands: NAG-NAG.32, NAG-NAG.32 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain L: N.269, I.290, V.408 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abernathy, M.E. et al., Antibody elicited by HIV-1 immunogen vaccination in macaques displaces Env fusion peptide and destroys a neutralizing epitope. Npj Vaccines (2021)

Release Date

2021-10-27

Peptides

8ANC195 G52K5 Fab heavy chain: AGJ
8ANC195 G52K5 Fab light chain: BIK
HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41: CDE
Envelope glycoprotein BG505 SOSIP.664 gp120: FHL
Ab1245 Fab heavy chain: M
Ab1245 Fab light chain: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
H

J
M

B
B

I
L

K
O

C
C

D
D

E
F

F
G

H
J

L
P

M
R

N
W

8ANC195 G52K5 Fab heavy chain

8ANC195 G52K5 Fab light chain

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41

Envelope glycoprotein BG505 SOSIP.664 gp120

Ab1245 Fab heavy chain

Ab1245 Fab light chain

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