SMTL ID : 6pw6.1

The HIV-1 Envelope Glycoprotein Clone BG505 SOSIP.664 in Complex with Three Copies of the Bovine Broadly Neutralizing Antibody, NC-Cow1, Fragment Antigen Binding Domain

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

24 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: 2 residues within 4Å: Chain A: T.133, N.157 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.153, Y.170, L.172, D.325 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.170 NAG-NAG.4: 6 residues within 4Å: Chain A: N.390, S.392, R.422 Ligands: NAG-NAG.5, NAG-NAG.5, NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: N.367, S.368, N.390, S.392 Ligands: NAG-NAG.4, NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: E.92, N.93 Chain B: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.281, T.283 Ligands: NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: K.237, N.239, T.241 Ligands: NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: L.270, P.296, N.451 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain D: T.133, N.157 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain D: N.153, Y.170, L.172, D.325 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.170 NAG-NAG.14: 6 residues within 4Å: Chain D: N.390, S.392, R.422 Ligands: NAG-NAG.15, NAG-NAG.15, NAG.46 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain D: N.367, S.368, N.390, S.392 Ligands: NAG-NAG.14, NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain D: E.92, N.93 Chain E: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain D: N.281, T.283 Ligands: NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain D: K.237, N.239, T.241 Ligands: NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain D: L.270, P.296, N.451 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain G: T.133, N.157 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain G: N.153, Y.170, L.172, D.325 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.170 NAG-NAG.24: 6 residues within 4Å: Chain G: N.390, S.392, R.422 Ligands: NAG-NAG.25, NAG-NAG.25, NAG.58 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 6 residues within 4Å: Chain G: N.367, S.368, N.390, S.392 Ligands: NAG-NAG.24, NAG-NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain G: E.92, N.93 Chain H: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain G: N.281, T.283 Ligands: NAG-NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain G: K.237, N.239, T.241 Ligands: NAG-NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain G: L.270, P.296, N.451 No protein-ligand interaction detected (PLIP)

6 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.3: 7 residues within 4Å: Chain A: P.217, N.267, N.381, C.382, G.383, V.449, S.450 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.383 NAG-NAG-BMA-MAN.9: 7 residues within 4Å: Chain A: R.197, N.202, T.203 Chain C: Q.115, Q.116, Y.117 Chain D: R.313 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.115, C:Y.117 NAG-NAG-BMA-MAN.13: 7 residues within 4Å: Chain D: P.217, N.267, N.381, C.382, G.383, V.449, S.450 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.383 NAG-NAG-BMA-MAN.19: 7 residues within 4Å: Chain D: R.197, N.202, T.203 Chain F: Q.115, Q.116, Y.117 Chain G: R.313 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.115, F:Y.117 NAG-NAG-BMA-MAN.23: 7 residues within 4Å: Chain G: P.217, N.267, N.381, C.382, G.383, V.449, S.450 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.383 NAG-NAG-BMA-MAN.29: 7 residues within 4Å: Chain A: R.313 Chain G: R.197, N.202, T.203 Chain I: Q.115, Q.116, Y.117 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Q.115, I:Y.117

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

NAG.31: 3 residues within 4Å: Chain A: N.306, I.327, V.445 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: Q.298, N.300, N.336, S.338 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: N.300, T.302, H.334, N.336 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: N.396 Ligands: NAG-NAG.4, NAG-NAG.4 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: R.354, N.359, N.360 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: T.137, N.138 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: N.141, N.142 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: N.343, W.399 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: W.99, N.100, S.102 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: E.110, N.114, M.115, Q.119 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: K.122, E.123, N.126 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.107, E.110 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain D: N.306, I.327, V.445 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain D: Q.298, N.300, N.336, S.338 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain D: N.300, T.302, H.334, N.336 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain D: N.396 Ligands: NAG-NAG.14, NAG-NAG.14 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain D: R.354, N.359, N.360 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: T.137, N.138 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: N.141, N.142 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain D: N.343, W.399 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: W.99, N.100, S.102 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain E: E.110, N.114, M.115, Q.119 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain E: K.122, E.123, N.126 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain E: N.107, E.110 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain G: N.306, I.327, V.445 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain G: Q.298, N.300, N.336, S.338 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain G: N.300, T.302, H.334, N.336 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain G: N.396 Ligands: NAG-NAG.24, NAG-NAG.24 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain G: R.354, N.359, N.360 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain G: T.137, N.138 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain G: N.141, N.142 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain G: N.343, W.399 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain H: W.99, N.100, S.102 Ligand excluded by PLIP NAG.64: 4 residues within 4Å: Chain H: E.110, N.114, M.115, Q.119 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain H: K.122, E.123, N.126 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain H: N.107, E.110 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stanfield, R.L. et al., Structural basis of broad HIV neutralization by a vaccine-induced cow antibody. Sci Adv (2020)

Release Date

2020-06-24

Peptides

Envelope glycoprotein gp120: ADG
Envelope glycoprotein gp41: BEH
Broadly Neutralizing Antibody NC-Cow1 Heavy Chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

G
E

B
B

E
D

H
F

C
G

F
H

I
I

Envelope glycoprotein gp120

Envelope glycoprotein gp41

Broadly Neutralizing Antibody NC-Cow1 Heavy Chain

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