SMTL ID : 5v8l.1

BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibodies 3BNC117 and PGT145

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-1-3-1-mer

Ligands

28 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: 5 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, T.18, D.113 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.18 NAG-NAG.2: 5 residues within 4Å: Chain A: N.103, R.113, K.117, K.159, Y.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.159 NAG-NAG.3: 5 residues within 4Å: Chain A: V.104, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.135 NAG-NAG.4: 7 residues within 4Å: Chain A: V.97, T.98, S.120, F.121, N.122, E.160 Chain J: D.79 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: J:D.79 Hydrogen bonds: A:E.160 NAG-NAG.8: 2 residues within 4Å: Chain A: Q.263, N.265 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain A: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain A: N.355, S.357, G.358 Ligands: NAG-NAG-BMA-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.103, G.114, K.159 Ligands: NAG-NAG-BMA-MAN-MAN.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.159 NAG-NAG.15: 3 residues within 4Å: Chain C: N.118, Y.135, D.290 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.135 NAG-NAG.17: 5 residues within 4Å: Chain C: R.162, N.167 Chain G: H.73, W.76, F.78 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain C: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain C: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain C: T.267, H.299, N.301, S.381 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG-BMA.24 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.18 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain D: E.57, N.58 Chain E: G.16, D.113 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain D: N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 7 residues within 4Å: Chain D: R.162, N.167, T.168 Chain I: H.73, A.74, W.76, F.78 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain D: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 2 residues within 4Å: Chain D: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 4 residues within 4Å: Chain D: T.267, H.299, N.301, S.381 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 1 residues within 4Å: Chain D: N.416 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 4 residues within 4Å: Chain E: K.122, E.123, S.125, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 1 residues within 4Å: Chain F: N.100 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 4 residues within 4Å: Chain K: T.20, W.63, E.66, N.68 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 5 residues within 4Å: Chain L: T.20, T.22, R.61, E.66, N.68 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 5 residues within 4Å: Chain M: T.20, T.22, R.61, E.66, N.68 No protein-ligand interaction detected (PLIP)

5 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: 5 residues within 4Å: Chain A: V.144, R.162, N.167 Chain H: H.73, W.76 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain A Hydrogen bonds: H:H.73 Hydrophobic interactions: A:V.144 NAG-NAG-BMA.10: 5 residues within 4Å: Chain A: T.267, R.296, H.299, N.301, S.381 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.296 NAG-NAG-BMA.16: 7 residues within 4Å: Chain C: Q.100, N.122, K.131 Chain J: D.129, Y.130, E.142 Chain N: H.27 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain N Hydrophobic interactions: J:D.129 Hydrogen bonds: N:H.27 NAG-NAG-BMA.24: 8 residues within 4Å: Chain C: N.332, N.355, S.357, P.385, R.387 Ligands: NAG-NAG-BMA-MAN-MAN.23, NAG-NAG-BMA-MAN-MAN.23, NAG-NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 7 residues within 4Å: Chain D: N.355, S.357, P.385 Ligands: NAG-NAG-BMA-MAN-MAN.36, NAG-NAG-BMA-MAN-MAN.36, NAG-NAG-BMA-MAN-MAN.36, NAG.59 No protein-ligand interaction detected (PLIP)

1 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.6: 11 residues within 4Å: Chain A: S.179, E.181, P.182, K.222, N.232, C.347, G.348, Q.408, V.414, S.415 Ligands: NAG-NAG.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348, A:V.414, A:E.181

1 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.7: 7 residues within 4Å: Chain A: E.245, N.246 Chain L: G.27, Y.28, R.62, W.63, G.64 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:Y.28 Hydrogen bonds: L:R.62

3 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.11: 4 residues within 4Å: Chain A: N.332, T.341 Ligands: NAG-NAG.12, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.23: 6 residues within 4Å: Chain C: N.332, N.355 Chain G: K.88 Ligands: NAG-NAG.14, NAG-NAG-BMA.24, NAG-NAG-BMA.24 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.88 NAG-NAG-BMA-MAN-MAN.36: 3 residues within 4Å: Chain D: N.332 Ligands: NAG-NAG-BMA.37, NAG-NAG-BMA.37 No protein-ligand interaction detected (PLIP)

2 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.18: 12 residues within 4Å: Chain C: S.179, E.181, K.222, V.224, L.231, N.232, C.347, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.26 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.348, C:V.414 NAG-NAG-BMA-MAN-MAN-MAN-MAN.31: 10 residues within 4Å: Chain D: S.179, E.181, K.222, V.224, L.231, N.232, G.348, C.413, V.414, S.415 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.348, D:E.181

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.19: 8 residues within 4Å: Chain C: T.206, E.245, N.246 Chain K: G.27, Y.28, R.62, W.63, Y.87 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:R.62 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.29: 12 residues within 4Å: Chain D: Q.100, N.122, K.131 Chain J: N.54, H.76, E.77, K.124, H.125, R.126, L.127 Chain N: T.33, H.58 3 PLIP interactions: 1 interactions with chain N, 2 interactions with chain J Hydrophobic interactions: N:T.33, J:L.127 Hydrogen bonds: J:R.126, J:R.126, N:H.58 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.32: 9 residues within 4Å: Chain D: E.245, N.246 Chain M: G.27, Y.28, R.62, W.63, G.64, Q.65, Y.87 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:R.62, M:R.62, M:R.62

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

NAG.44: 1 residues within 4Å: Chain A: N.204 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain A: N.308, E.309 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain A: N.361 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain B: N.100 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain B: N.107, S.109, E.110, N.114 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain B: N.126, Y.127 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: E.57, N.58 Chain F: G.16 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.204 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.308 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain D: N.103 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain D: N.204 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain D: N.308 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain D: N.324 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain D: N.361 Ligands: NAG-NAG-BMA.37 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain E: N.100 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain E: N.107, S.109 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain F: N.107, S.109, E.110 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain F: E.123, 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: ACD
gp41: BEF
3BNC117 antibody, heavy chain: GHI
PGT145 antibody, heavy chain: J
3BNC117 antibody, light chain: KLM
PGT145 antibody, light chain: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

B
B

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

gp120

gp41

3BNC117 antibody, heavy chain

PGT145 antibody, heavy chain

3BNC117 antibody, light chain

PGT145 antibody, light chain

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