SMTL ID : 5cjx.1

Crystal structure of 8ANC195 Fab in complex with BG505 SOSIP.664 HIV-1 Env trimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.58 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

2 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.1: 9 residues within 4Å: Chain B: S.125, N.126 Chain G: S.109 Chain J: Y.50, R.51, A.53, A.54, L.55, S.61 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:Y.50, J:A.53 NAG-NAG-BMA-MAN-MAN.16: 9 residues within 4Å: Chain D: Q.1, H.3, V.5, Y.25, S.77, P.79 Chain L: N.244, T.246, N.247 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain D Hydrophobic interactions: L:T.246 Hydrogen bonds: D:Q.1, D:Q.1

5 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: 5 residues within 4Å: Chain F: Q.261, N.263, V.300, S.301, V.412 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain F: P.180, V.222, N.230, N.344, V.412, S.413 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:V.412 NAG-NAG.6: 2 residues within 4Å: Chain G: N.88, T.90 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain H: N.107 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain E: A.68 Chain K: N.100, S.102 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.68

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.4: 19 residues within 4Å: Chain F: K.200, N.202, I.245, H.319 Chain G: T.19, W.55, S.57, S.58, A.59, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, S.83, E.85 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:A.71, G:D.73 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.9: 21 residues within 4Å: Chain A: T.19, W.55, S.57, S.58, A.59, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.82, S.83, E.85 Chain I: N.202, I.245, H.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.71, A:D.73 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.14: 20 residues within 4Å: Chain D: T.19, W.55, S.57, S.58, A.59, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, S.83, E.85 Chain L: K.200, N.202, I.245, H.319 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.73

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.5: 9 residues within 4Å: Chain F: N.244, T.246, N.247 Chain G: Q.1, H.3, Y.25, G.26, P.79, Q.124 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:T.246 Hydrogen bonds: G:Q.1 NAG-NAG-BMA-MAN-MAN-MAN.11: 8 residues within 4Å: Chain A: Q.1, H.3, Y.25, G.26, P.79 Chain I: N.244, T.246, N.247 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain I Hydrogen bonds: A:Q.1, A:G.26 Hydrophobic interactions: I:T.246

2 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.8: 9 residues within 4Å: Chain A: W.108, G.110 Chain C: N.32, Y.50, R.51, A.53, A.54 Chain H: S.125, N.126 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.50, C:A.53, A:G.110 NAG-NAG-BMA-MAN.13: 8 residues within 4Å: Chain D: W.108, S.109 Chain E: Y.50, R.51, A.53, A.54 Chain K: S.125, N.126 No protein-ligand interaction detected (PLIP)

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.10: 7 residues within 4Å: Chain I: P.180, V.222, N.230, N.344, C.411, V.412, S.413 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:V.412 Hydrogen bonds: I:V.412 NAG-NAG-BMA.15: 6 residues within 4Å: Chain L: P.180, V.222, N.230, V.412, S.413 Ligands: NAG.22 No protein-ligand interaction detected (PLIP)

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

NAG.17: 2 residues within 4Å: Chain A: G.15, N.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.15, A:N.88 NAG.18: 4 residues within 4Å: Chain B: N.100, S.102, W.103, I.130 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.130 Hydrogen bonds: B:N.100, B:S.102, B:W.103 NAG.19: 4 residues within 4Å: Chain H: N.100, S.102, W.103, Y.127 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.102 NAG.20: 3 residues within 4Å: Chain I: Q.261, N.263, V.412 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain L: N.263, V.412 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.263 NAG.22: 4 residues within 4Å: Chain L: L.233, P.259, N.414 Ligands: NAG-NAG-BMA.15 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:L.233, L:P.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scharf, L. et al., Broadly Neutralizing Antibody 8ANC195 Recognizes Closed and Open States of HIV-1 Env. Cell (2015)

Release Date

2015-09-23

Peptides

8ANC195 G52K5 heavy chain, IG gamma-1 chain: ADG
BG505 Env gp41: BHK
8ANC195 G52K5 light chain: CEJ
BG505 Env gp120: FIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
H

B
B

H
J

K
X

C
C

E
E

J
L

F
G

I
K

L
Y

8ANC195 G52K5 heavy chain, IG gamma-1 chain

BG505 Env gp41

8ANC195 G52K5 light chain

BG505 Env gp120

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