SMTL ID : 5v8m.1

BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibody 3BNC117

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 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.1: 4 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, D.113 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 4 residues within 4Å: Chain E: E.57, N.58 Chain F: G.16, D.113 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 4 residues within 4Å: Chain I: E.57, N.58 Chain J: G.16, D.113 No protein-ligand interaction detected (PLIP)

24 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: 4 residues within 4Å: Chain A: N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: Q.100, S.120, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: R.162, N.167 Chain C: H.73, W.76, F.78 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain A: N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain D: R.61, W.63, E.66, N.68 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain E: N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: Q.100, S.120, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain E: R.162, N.167 Chain G: H.73, W.76, F.78 Chain I: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain E: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain E: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain E: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain E: N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.18 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain H: R.61, W.63, E.66, N.68 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain I: N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain I: Q.100, S.120, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 6 residues within 4Å: Chain A: R.278 Chain I: R.162, N.167 Chain K: H.73, W.76, F.78 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain I: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 2 residues within 4Å: Chain I: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 5 residues within 4Å: Chain I: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 2 residues within 4Å: Chain I: N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.31 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 4 residues within 4Å: Chain L: R.61, W.63, E.66, N.68 No protein-ligand interaction detected (PLIP)

3 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.5: 11 residues within 4Å: Chain A: E.181, P.182, K.222, V.224, L.231, N.232, C.347, G.348, V.414, S.415 Ligands: NAG-NAG.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.181, A:G.348, A:V.414 NAG-NAG-BMA-MAN-MAN-MAN-MAN.18: 11 residues within 4Å: Chain E: E.181, P.182, K.222, V.224, L.231, N.232, C.347, G.348, V.414, S.415 Ligands: NAG-NAG.25 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.181, E:G.348, E:V.414 NAG-NAG-BMA-MAN-MAN-MAN-MAN.31: 11 residues within 4Å: Chain I: E.181, P.182, K.222, V.224, L.231, N.232, C.347, G.348, V.414, S.415 Ligands: NAG-NAG.38 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:E.181, I:G.348, I:V.414

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN.6: 6 residues within 4Å: Chain A: N.246 Chain D: G.27, Y.28, R.62, W.63, G.64 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.62, D:R.62 Hydrophobic interactions: D:Y.28 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.19: 6 residues within 4Å: Chain E: N.246 Chain H: G.27, Y.28, R.62, W.63, G.64 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.62, H:R.62 Hydrophobic interactions: H:Y.28 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.32: 6 residues within 4Å: Chain I: N.246 Chain L: G.27, Y.28, R.62, W.63, G.64 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:R.62, L:R.62 Hydrophobic interactions: L:Y.28

3 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.10: 5 residues within 4Å: Chain A: N.332, T.341 Chain C: K.88 Ligands: NAG-NAG-BMA-MAN.11, NAG-NAG-BMA-MAN.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.88 NAG-NAG-BMA-MAN-MAN-MAN.23: 5 residues within 4Å: Chain E: N.332, T.341 Chain G: K.88 Ligands: NAG-NAG-BMA-MAN.24, NAG-NAG-BMA-MAN.24 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.88 NAG-NAG-BMA-MAN-MAN-MAN.36: 5 residues within 4Å: Chain I: N.332, T.341 Chain K: K.88 Ligands: NAG-NAG-BMA-MAN.37, NAG-NAG-BMA-MAN.37 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:K.88

3 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.11: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.10, NAG-NAG-BMA-MAN-MAN-MAN.10, NAG.44 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.24: 5 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.23, NAG-NAG-BMA-MAN-MAN-MAN.23, NAG.51 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.37: 5 residues within 4Å: Chain I: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.36, NAG-NAG-BMA-MAN-MAN-MAN.36, NAG.58 No protein-ligand interaction detected (PLIP)

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

NAG.40: 1 residues within 4Å: Chain A: N.103 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: K.202, N.204 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain A: N.308 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG-BMA-MAN.11 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain B: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain E: N.103 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: K.202, N.204 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG-BMA-MAN.24 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain F: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain I: N.103 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain I: K.202, N.204 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain I: N.308 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain I: N.324 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain I: N.361 Ligands: NAG-NAG-BMA-MAN.37 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain J: N.100, S.102 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain J: K.122, E.123, S.125, N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J.H. et al., A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic beta-Hairpin Structure. Immunity (2017)

Release Date

2017-05-03

Peptides

gp120: AEI
gp41: BFJ
antibody 3BNC117, heavy chain: CGK
antibody 3BNC117, light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
F

I
G

B
B

F
I

J
J

C
H

G
R

K
S

D
L

H
T

L
U

gp120

gp41

antibody 3BNC117, heavy chain

antibody 3BNC117, light chain

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