SMTL ID : 6tyb.1

Isolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan Shields

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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.1: 6 residues within 4Å: Chain A: N.37 Chain C: A.72, D.73, R.74, S.75, Q.82 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.74 NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 14 residues within 4Å: Chain A: R.155, D.156, N.157, R.213, T.215, W.319, I.320, D.321, G.322 Chain B: Q.33, N.88 Chain D: S.30, S.67, G.68 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.6: 12 residues within 4Å: Chain A: G.216, T.217, N.218 Chain D: R.18, T.20, Y.52, G.64, G.65, G.66, S.67, T.72, T.74 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.66, D:S.67

1 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.4, N.46 No protein-ligand interaction detected (PLIP)

1 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: 4 residues within 4Å: Chain A: E.33, A.35, N.106, V.121 No protein-ligand interaction detected (PLIP)

1 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.4: 10 residues within 4Å: Chain A: H.85, Y.86, D.88, Q.132, N.140, R.243, C.306, N.307, S.308 Ligands: NAG.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.307 Hydrogen bonds: A:Y.86, A:N.307

2 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.7: 7 residues within 4Å: Chain A: N.146, N.164, Y.166, Y.167, E.203 Chain D: N.56, G.57 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.167 NAG-NAG-BMA-MAN-MAN-MAN.8: 10 residues within 4Å: Chain A: K.202, K.205, T.220, D.221, I.223, N.224, E.259, D.260, R.261, N.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.259, A:D.260 Water bridges: A:N.262

1 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: 8 residues within 4Å: Chain A: T.226, D.318, W.319, N.326 Chain B: N.30, N.32, I.34, P.48 No protein-ligand interaction detected (PLIP)

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

NAG.10: 3 residues within 4Å: Chain A: Y.166, N.168, K.196 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.166, A:K.196 Hydrogen bonds: A:Y.166, A:N.168 NAG.11: 4 residues within 4Å: Chain A: K.172, T.305, N.307 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, J. et al., Isolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan Shields. Immunity (2019)

Release Date

2019-10-02

Peptides

Envelope glycoprotein gp160: A
T-cell surface glycoprotein CD4: B
NEUTRALIZING ANTIBODY ITS90.03 FAB HEAVY CHAIN: C
NEUTRALIZING ANTIBODY ITS90.03 FAB LIGHT CHAIN: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
C

C
H

D
L

Envelope glycoprotein gp160

T-cell surface glycoprotein CD4

NEUTRALIZING ANTIBODY ITS90.03 FAB HEAVY CHAIN

NEUTRALIZING ANTIBODY ITS90.03 FAB LIGHT CHAIN