SMTL ID : 5esv.1

Crystal Structure of Broadly Neutralizing Antibody CH03, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade C Superinfecting Strain of Donor CAP256.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

hetero-3-3-3-mer

Ligands

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.1: 9 residues within 4Å: Chain A: I.28, E.30, N.31 Chain E: N.41, K.56, Y.58, L.60 Chain G: K.53, T.187 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:Y.58, A:E.30 Hydrogen bonds: A:E.30

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.2: 15 residues within 4Å: Chain A: M.51, N.54, G.55, G.56, T.58, Y.60, S.69, M.70, S.71, R.72 Chain E: N.20, S.77, E.78 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.72 Hydrogen bonds: A:Y.60

5 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.3: 25 residues within 4Å: Chain E: N.27, I.28, N.29 Chain H: R.59, I.104, D.105, D.106, Q.107, G.108, W.118 Chain I: Q.27, S.28, V.29, H.30, P.31, Y.33, S.68, G.69, Y.92, G.93, G.94, S.95, Y.97 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN-MAN-MAN.11 5 PLIP interactions: 1 interactions with chain I, 4 interactions with chain H Hydrogen bonds: I:Y.33, H:D.106, H:R.59, H:R.59, H:I.104, H:W.118, I:Y.92 NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 20 residues within 4Å: Chain A: N.52, W.53, N.54, G.56, D.57, R.59, T.103, I.104, D.105, Y.111, S.114, T.116 Chain B: S.95 Chain E: S.43, F.44, N.45, K.56, E.57 Ligands: NAG-NAG-BMA-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.103 Hydrogen bonds: A:N.54, A:T.103 NAG-NAG-BMA-MAN-MAN-MAN-MAN.7: 19 residues within 4Å: Chain A: R.59, I.104, D.105, D.106, Q.107, G.108, W.118 Chain B: H.30, P.31, Y.33, Y.92, G.93, G.94, S.95, Y.97 Chain F: N.27, N.29 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN.4 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.33, B:G.93, B:Y.92, B:Y.97, A:R.59, A:R.59, A:D.106, A:W.118 NAG-NAG-BMA-MAN-MAN-MAN-MAN.8: 22 residues within 4Å: Chain C: N.52, W.53, N.54, G.56, D.57, R.59, T.103, I.104, D.105, Y.111, S.114 Chain D: E.1, S.95 Chain F: S.43, F.44, N.45, K.56, E.57 Ligands: NAG-NAG-BMA.6, NAG-NAG-BMA.6, NAG-NAG-BMA.6, NAG-NAG-BMA-MAN-MAN-MAN.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.52, C:N.54, C:G.56, C:D.57, C:T.103, C:G.56 NAG-NAG-BMA-MAN-MAN-MAN-MAN.11: 22 residues within 4Å: Chain G: S.43, F.44, N.45, K.56 Chain H: N.52, W.53, N.54, G.56, D.57, R.59, T.103, I.104, D.105, Y.111, S.114, T.116 Chain I: E.1, S.95 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN-MAN.9, NAG-NAG-BMA-MAN-MAN-MAN.9, NAG-NAG-BMA-MAN-MAN-MAN.9 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:N.54, H:N.54, H:T.103

2 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.5: 9 residues within 4Å: Chain C: I.28, E.30, N.77 Chain E: E.49, L.50 Chain F: N.41, Y.58, A.59, L.60 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 8 residues within 4Å: Chain C: N.54, G.55, G.56, S.71, R.72 Chain F: N.20 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.8, NAG-NAG-BMA-MAN-MAN-MAN-MAN.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.54

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.9: 15 residues within 4Å: Chain G: N.20, S.77, E.78 Chain H: N.54, G.55, G.56, T.58, Y.60, S.71, R.72, D.73, N.74 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.10: 25 residues within 4Å: Chain C: R.59, I.104, D.105, D.106, Q.107, G.108, W.118 Chain D: S.28, H.30, P.31, Y.33, S.68, G.69, Y.92, G.93, G.94, S.95, Y.97 Chain F: D.52 Chain G: K.25, V.26, N.27, N.29 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.8, NAG-NAG-BMA-MAN-MAN-MAN-MAN.8 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.106, D:Y.92, D:S.95, C:R.59, C:R.59, C:D.106, C:W.118

3 x ZN: ZINC ION(Non-covalent)

ZN.12: 3 residues within 4Å: Chain E: D.10, H.12, H.95 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.10, E:D.10, E:H.12, E:H.95 ZN.13: 3 residues within 4Å: Chain F: D.10, H.12, H.95 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.10, F:D.10, F:H.12, F:H.95 ZN.15: 3 residues within 4Å: Chain G: D.10, H.12, H.95 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.10, G:H.12

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

NAG.14: 5 residues within 4Å: Chain G: N.41, Y.58, A.59, L.60 Chain H: E.30 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:L.60 Hydrogen bonds: H:E.30, H:E.30

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

CH03 Heavy Chain: ACH
CH03 Light Chain: BDI
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase,Envelope glycoprotein gp160: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

H
H

B
B

D
D

I
L

E
E

F
F

G
G

CH03 Heavy Chain

CH03 Light Chain

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