SMTL ID : 7n65.1

Complex structure of HIV superinfection Fab QA013.2 and BG505.SOSIP.664

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

18 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: 2 residues within 4Å: Chain A: E.92, N.93 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: N.153, Y.170, L.172, G.324, D.325 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 2 residues within 4Å: Chain A: Q.135, N.157 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 3 residues within 4Å: Chain A: N.281, T.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 6 residues within 4Å: Chain A: N.367, S.368, N.390, S.392 Ligands: NAG-NAG-BMA.14, NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 4 residues within 4Å: Chain A: N.390, S.392 Ligands: NAG-NAG-BMA.13, NAG-NAG-BMA.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 2 residues within 4Å: Chain E: E.92, N.93 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 5 residues within 4Å: Chain E: N.153, Y.170, L.172, G.324, D.325 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 2 residues within 4Å: Chain E: Q.135, N.157 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 3 residues within 4Å: Chain E: N.281, T.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 6 residues within 4Å: Chain E: N.367, S.368, N.390, S.392 Ligands: NAG-NAG-BMA.31, NAG-NAG-BMA.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 4 residues within 4Å: Chain E: N.390, S.392 Ligands: NAG-NAG-BMA.30, NAG-NAG-BMA.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 2 residues within 4Å: Chain I: E.92, N.93 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 5 residues within 4Å: Chain I: N.153, Y.170, L.172, G.324, D.325 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.38: 2 residues within 4Å: Chain I: Q.135, N.157 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.42: 3 residues within 4Å: Chain I: N.281, T.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.47: 6 residues within 4Å: Chain I: N.367, S.368, N.390, S.392 Ligands: NAG-NAG-BMA.48, NAG-NAG-BMA.48 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.48: 4 residues within 4Å: Chain I: N.390, S.392 Ligands: NAG-NAG-BMA.47, NAG-NAG-BMA.47 No protein-ligand interaction detected (PLIP)

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.2: 2 residues within 4Å: Chain A: N.138, K.152 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: R.197, N.202, T.203 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: N.239, S.279, E.280, I.282, H.356 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain A: G.358, N.359 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain A: G.393, N.396 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain A: P.296, V.449, S.450, N.451 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain A: R.507, V.508 Chain B: N.108, S.110, W.111 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain E: N.138, K.152 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain E: R.197, N.202, T.203 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain E: N.239, S.279, E.280, I.282, H.356 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain E: G.358, N.359 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain E: G.393, N.396 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain E: P.296, V.449, S.450, N.451 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 5 residues within 4Å: Chain E: R.507, V.508 Chain F: N.108, S.110, W.111 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 2 residues within 4Å: Chain I: N.138, K.152 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain I: R.197, N.202, T.203 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 5 residues within 4Å: Chain I: N.239, S.279, E.280, I.282, H.356 No protein-ligand interaction detected (PLIP) NAG-NAG.46: 2 residues within 4Å: Chain I: G.358, N.359 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 2 residues within 4Å: Chain I: G.393, N.396 No protein-ligand interaction detected (PLIP) NAG-NAG.50: 5 residues within 4Å: Chain I: P.296, V.449, S.450, N.451 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.41 No protein-ligand interaction detected (PLIP) NAG-NAG.51: 5 residues within 4Å: Chain I: R.507, V.508 Chain J: N.108, S.110, W.111 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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: 15 residues within 4Å: Chain A: Y.66, E.67, T.68, E.216, K.257, L.266, N.267, F.380, N.381, C.382, G.383, R.447, C.448, V.449 Ligands: NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.24: 15 residues within 4Å: Chain E: Y.66, E.67, T.68, E.216, K.257, L.266, N.267, F.380, N.381, C.382, G.383, R.447, C.448, V.449 Ligands: NAG-NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.41: 15 residues within 4Å: Chain I: Y.66, E.67, T.68, E.216, K.257, L.266, N.267, F.380, N.381, C.382, G.383, R.447, C.448, V.449 Ligands: NAG-NAG.50 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.9: 4 residues within 4Å: Chain A: Q.298, N.300, N.336, R.447 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.26: 4 residues within 4Å: Chain E: Q.298, N.300, N.336, R.447 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.43: 4 residues within 4Å: Chain I: Q.298, N.300, N.336, R.447 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.10: 10 residues within 4Å: Chain A: N.306, I.327 Chain C: D.1, E.26, L.27, G.28, F.29, R.30, R.31, N.77 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.29, C:F.29 NAG-NAG-BMA-MAN-MAN-MAN-MAN.27: 10 residues within 4Å: Chain E: N.306, I.327 Chain G: D.1, E.26, L.27, G.28, F.29, R.30, R.31, N.77 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:F.29, G:F.29 NAG-NAG-BMA-MAN-MAN-MAN-MAN.44: 10 residues within 4Å: Chain I: N.306, I.327 Chain K: D.1, E.26, L.27, G.28, F.29, R.30, R.31, N.77 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:F.29, K:F.29

3 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: 14 residues within 4Å: Chain A: N.300, R.331, N.336, R.447 Chain C: W.33, E.99, Y.105, R.108, I.109, P.110, G.112, N.113 Chain D: Y.93 Ligands: MAN.55 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:R.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.28: 13 residues within 4Å: Chain E: N.300, R.331, N.336, R.447 Chain G: W.33, E.99, Y.105, R.108, I.109, P.110, N.113 Chain H: Y.93 Ligands: MAN.59 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:R.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.45: 13 residues within 4Å: Chain I: N.300, R.331, N.336, R.447 Chain K: W.33, E.99, Y.105, R.108, I.109, P.110, G.112, N.113 Ligands: MAN.63 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:R.108

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

NAG.52: 2 residues within 4Å: Chain A: K.339, N.343 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.339, A:N.343 NAG.53: 1 residues within 4Å: Chain B: N.115 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.115 NAG.54: 3 residues within 4Å: Chain B: E.131, N.134, Y.135 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.134, B:Y.135 NAG.56: 2 residues within 4Å: Chain E: K.339, N.343 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.339, E:N.343 NAG.57: 1 residues within 4Å: Chain F: N.115 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.115 NAG.58: 3 residues within 4Å: Chain F: E.131, N.134, Y.135 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.134, F:Y.135 NAG.60: 2 residues within 4Å: Chain I: K.339, N.343 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:K.339, I:N.343 NAG.61: 1 residues within 4Å: Chain J: N.115 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.115 NAG.62: 3 residues within 4Å: Chain J: E.131, N.134, Y.135 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.134, J:Y.135

3 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.55: 7 residues within 4Å: Chain C: D.50, K.59 Chain D: Y.93, L.97, T.98, A.99 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.50 MAN.59: 7 residues within 4Å: Chain G: D.50, K.59 Chain H: Y.93, L.97, T.98, A.99 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.28 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.50 MAN.63: 6 residues within 4Å: Chain K: D.50, K.59 Chain L: Y.93, T.98, A.99 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.45 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:D.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shipley, M.M. et al., Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection. Elife (2021)

Release Date

2021-07-28

Peptides

Envelope glycoprotein gp41: AEI
Envelope glycoprotein gp41: BFJ
Fab QA013.2 Heavy Chain, variable region: CGK
Fab QA013.2 Light Chain, , variable region: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

B
B

F
F

J
J

C
C

G
G

K
K

D
D

H
H

L
L

Envelope glycoprotein gp41

Envelope glycoprotein gp41

Fab QA013.2 Heavy Chain, variable region

Fab QA013.2 Light Chain, , variable region

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