SMTL ID : 5viy.1

BG505 SOSIP.664 in complex with broadly neutralizing antibodies BG1 and 8ANC195

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 6.20 Å

Oligo State

hetero-3-3-2-2-3-3-mer

Ligands

9 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: 4 residues within 4Å: Chain A: S.125, N.126 Chain N: N.32, A.53 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:A.53 NAG-NAG-BMA-MAN-MAN.2: 5 residues within 4Å: Chain B: S.125, N.126 Chain L: N.32, A.53, L.55 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:A.53 NAG-NAG-BMA-MAN-MAN.3: 5 residues within 4Å: Chain C: K.122, S.125, N.126 Chain P: N.32, A.53 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:A.53 NAG-NAG-BMA-MAN-MAN.5: 7 residues within 4Å: Chain D: V.104, N.118, Y.135 Chain J: G.26, Y.28, W.54, Y.107 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.24: 7 residues within 4Å: Chain E: N.246, T.248, N.249 Chain O: Q.1, H.3, Y.25, G.26 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:H.3, O:Q.1 NAG-NAG-BMA-MAN-MAN.32: 10 residues within 4Å: Chain F: V.104, N.118, Y.135, L.137 Chain H: G.26, F.27, Y.28, D.31, W.54, Y.107 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Y.28, H:E.2, H:D.31, H:D.31 NAG-NAG-BMA-MAN-MAN.33: 12 residues within 4Å: Chain F: Q.100, S.120, F.121, N.122, K.133 Chain H: R.52, Q.61, Q.111, E.112, G.113, F.114 Chain I: F.28 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Q.61, H:G.113, H:R.52, H:F.114 NAG-NAG-BMA-MAN-MAN.37: 7 residues within 4Å: Chain F: N.246, T.248, N.249 Chain M: Q.1, H.3, Y.25, G.26 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:H.3, M:Q.1, M:Q.1 NAG-NAG-BMA-MAN-MAN.44: 15 residues within 4Å: Chain D: Q.100, N.122, K.131, K.133 Chain I: H.92, S.93, P.94 Chain J: R.52, A.55, Q.61, Q.111, E.112, G.113, F.114, G.115 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:Q.61, J:G.113, J:F.114

18 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 3 residues within 4Å: Chain B: G.16 Chain D: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain D: Q.263, N.265, N.301, V.302, S.303, S.381, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain D: N.271, I.292, Q.408, G.409 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 7 residues within 4Å: Chain D: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA.14, NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain D: N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: G.16 Chain E: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain E: N.103, D.111, G.114 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain E: R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 7 residues within 4Å: Chain E: Q.263, N.265, N.301, V.302, S.303, S.381, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain E: N.271, I.292, G.409 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 6 residues within 4Å: Chain E: N.265, T.267, R.296, H.299, N.301, T.383 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.296 NAG-NAG.31: 3 residues within 4Å: Chain A: G.16 Chain F: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain F: I.146, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 7 residues within 4Å: Chain F: Q.263, N.265, N.301, V.302, S.303, S.381, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 4 residues within 4Å: Chain F: N.271, I.292, Q.408, G.409 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 5 residues within 4Å: Chain F: N.265, T.267, H.299, N.301, T.383 No protein-ligand interaction detected (PLIP)

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.7: 6 residues within 4Å: Chain D: N.204 Chain K: W.55, S.70, A.71, V.72, D.73 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.70, K:A.71, K:A.71, K:D.73 NAG-NAG-BMA-MAN.22: 6 residues within 4Å: Chain E: N.204 Chain O: W.55, S.70, A.71, V.72, D.73 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:S.70, O:A.71, O:A.71, O:D.73 NAG-NAG-BMA-MAN.35: 7 residues within 4Å: Chain F: N.204, H.321 Chain M: W.55, S.70, A.71, V.72, D.73 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:A.71

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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.8: 8 residues within 4Å: Chain D: K.35, N.232, N.346, G.348, I.407, C.413, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.23: 9 residues within 4Å: Chain E: L.231, N.232, N.346, C.347, G.348, Q.408, C.413, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.36: 10 residues within 4Å: Chain F: L.231, N.232, N.346, C.347, G.348, I.407, Q.408, C.413, V.414, S.415 No protein-ligand interaction detected (PLIP)

2 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.9: 8 residues within 4Å: Chain D: N.246, T.248, N.249 Chain K: Q.1, H.3, Y.25, G.26, P.79 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:H.3, K:Q.1, K:Q.1, K:G.26 NAG-NAG-BMA-MAN.12: 6 residues within 4Å: Chain D: N.265, T.267, R.296, H.299, N.301, T.383 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.296

7 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.14: 4 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG-NAG.13, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 4 residues within 4Å: Chain D: P.261, V.262, Q.263, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain E: V.104, N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 6 residues within 4Å: Chain E: N.332, S.333, T.341, N.355, S.357 Ligands: NAG.53 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 8 residues within 4Å: Chain F: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA.42, NAG-NAG-BMA.42, NAG-NAG-BMA.42 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.42: 4 residues within 4Å: Chain F: N.355, S.357 Ligands: NAG-NAG-BMA.41, NAG-NAG-BMA.41 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.43: 4 residues within 4Å: Chain F: P.261, V.262, Q.263, N.416 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.29: 1 residues within 4Å: Chain E: N.361 No protein-ligand interaction detected (PLIP)

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.30: 4 residues within 4Å: Chain E: P.261, V.262, Q.263, N.416 No protein-ligand interaction detected (PLIP)

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

NAG.45: 2 residues within 4Å: Chain A: N.100, W.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.103 NAG.46: 2 residues within 4Å: Chain B: N.100, W.103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.103 NAG.47: 2 residues within 4Å: Chain C: N.100, W.103 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.103 NAG.48: 1 residues within 4Å: Chain D: N.103 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.103 NAG.49: 2 residues within 4Å: Chain D: N.308, W.364 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.364 NAG.50: 1 residues within 4Å: Chain D: N.324 No protein-ligand interaction detected (PLIP) NAG.51: 2 residues within 4Å: Chain E: N.308, W.364 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.308 NAG.52: 1 residues within 4Å: Chain E: N.324 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.324 NAG.53: 4 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG-BMA.28, NAG-NAG-BMA.28 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.357 NAG.54: 6 residues within 4Å: Chain F: N.103, D.111, G.114, K.117, R.140, K.159 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.117, F:R.140, F:R.140 NAG.55: 2 residues within 4Å: Chain F: N.308, W.364 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:W.364 Hydrogen bonds: F:N.308 NAG.56: 1 residues within 4Å: Chain F: N.324 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.324 NAG.57: 1 residues within 4Å: Chain F: N.361 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.361

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Asymmetric recognition of HIV-1 Envelope trimer by V1V2 loop-targeting antibodies. Elife (2017)

Release Date

2017-06-21

Peptides

Envelope glycoprotein gp160: ABC
Envelope glycoprotein gp160: DEF
BG1 Fab light chain: GI
BG1 Fab heavy chain: HJ
8ANC195 G52K5 Fab heavy chain: KMO
8ANC195 G52K5 Fab light chain: LNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

I
I

H
H

J
J

K
K

M
M

O
O

L
L

N
N

P
P

Envelope glycoprotein gp160

Envelope glycoprotein gp160

BG1 Fab light chain

BG1 Fab heavy chain

8ANC195 G52K5 Fab heavy chain

8ANC195 G52K5 Fab light chain

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