SMTL ID : 5esz.4 (3 other biounits)

Crystal Structure of Broadly Neutralizing Antibody CH04, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade AE Strain A244

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.19 Å

Oligo State

hetero-3-3-3-mer

Ligands

3 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: 4 residues within 4Å: Chain A: N.53, Q.67, H.70 Chain B: E.30 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: N.53, Q.67, H.70 Chain E: E.30 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain G: N.53, Q.67, H.70 Chain H: E.30 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: 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.2: 7 residues within 4Å: Chain A: T.18, H.20, N.57, K.66 Chain B: R.59 Chain C: R.94 Ligands: NAG-NAG-BMA-MAN.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.18 NAG-NAG-BMA-MAN-MAN-MAN.5: 7 residues within 4Å: Chain D: T.18, H.20, N.57, K.66 Chain E: R.59 Chain F: R.94 Ligands: NAG-NAG-BMA-MAN.6 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:T.18 NAG-NAG-BMA-MAN-MAN-MAN.8: 7 residues within 4Å: Chain G: T.18, H.20, N.57, K.66 Chain H: R.59 Chain I: R.94 Ligands: NAG-NAG-BMA-MAN.9 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:T.18

3 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.3: 10 residues within 4Å: Chain B: R.59, D.105, D.106, Q.107, G.108, W.118 Chain C: Y.33, G.93, Y.97 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.2 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:R.32, B:D.106, C:G.93, B:D.105, B:D.106, B:R.59, B:R.59, B:W.118, C:G.93 NAG-NAG-BMA-MAN.6: 10 residues within 4Å: Chain E: R.59, D.105, D.106, Q.107, G.108, W.118 Chain F: Y.33, G.93, Y.97 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.5 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:R.32, E:D.106, E:D.105, E:D.106, F:G.93, E:R.59, E:R.59, E:W.118, F:G.93 NAG-NAG-BMA-MAN.9: 10 residues within 4Å: Chain H: R.59, D.105, D.106, Q.107, G.108, W.118 Chain I: Y.33, G.93, Y.97 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.8 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:D.106, I:R.32, I:G.93, H:D.105, H:D.106, H:R.59, H:R.59, H:W.118, I:G.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, J. et al., Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design. Nat. Struct. Mol. Biol. (2016)

Release Date

2015-12-16

Peptides

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase,Envelope glycoprotein gp160: ADG
CH04 Heavy Chain: BEH
CH04 Light Chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

D
C

G
C

B
A

E
A

H
A

C
B

F
B

I
B

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase,Envelope glycoprotein gp160

CH04 Heavy Chain

CH04 Light Chain

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