SMTL ID : 6dfg.1

BG505 MD39 SOSIP trimer in complex with mature BG18 fragment antigen binding

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 2 residues within 4Å: Chain A: N.103, D.111 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.11: 2 residues within 4Å: Chain E: N.103, D.111 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.21: 2 residues within 4Å: Chain I: N.103, D.111 No protein-ligand interaction detected (PLIP)

15 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.135 NAG-NAG.3: 3 residues within 4Å: Chain A: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain A: Q.332, T.342, N.355, S.357, R.387 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.135 NAG-NAG.13: 3 residues within 4Å: Chain E: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain E: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 6 residues within 4Å: Chain E: Q.332, T.342, N.355, S.357, R.387 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.19 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain E: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain I: N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Y.135 NAG-NAG.23: 3 residues within 4Å: Chain I: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain I: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 6 residues within 4Å: Chain I: Q.332, T.342, N.355, S.357, R.387 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.29 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain I: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.24 No protein-ligand interaction detected (PLIP)

3 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.4: 8 residues within 4Å: Chain A: P.182, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.14: 8 residues within 4Å: Chain E: P.182, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.24: 8 residues within 4Å: Chain I: P.182, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.30 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:V.414

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.6: 3 residues within 4Å: Chain A: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 3 residues within 4Å: Chain E: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 3 residues within 4Å: Chain I: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP)

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.7: 18 residues within 4Å: Chain A: T.267, D.294, R.296, H.299, N.301 Chain C: V.2, D.27, S.28, R.29, H.33, R.98, R.102, I.103, G.105, V.106, V.107, F.113 Chain D: S.51 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.107 Hydrogen bonds: C:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.17: 18 residues within 4Å: Chain E: T.267, D.294, R.296, H.299, N.301 Chain G: V.2, D.27, S.28, R.29, H.33, R.98, R.102, I.103, G.105, V.106, V.107, F.113 Chain H: S.51 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.29, G:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.27: 19 residues within 4Å: Chain I: T.267, D.294, R.296, H.299, N.301, S.381 Chain K: V.2, D.27, S.28, R.29, H.33, R.98, R.102, I.103, G.105, V.106, V.107, F.113 Chain L: S.51 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:V.107

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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: 10 residues within 4Å: Chain A: N.361 Chain C: D.51, H.53, A.57, T.59, W.112, H.114 Chain D: D.94, K.97 Ligands: NAG-NAG.8 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.51, D:K.97, D:K.97 NAG-NAG-BMA-MAN-MAN-MAN.19: 11 residues within 4Å: Chain E: N.361 Chain G: D.51, H.53, N.55, A.57, T.59, W.112, H.114 Chain H: D.94, K.97 Ligands: NAG-NAG.18 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:D.51, H:K.97, H:K.97 NAG-NAG-BMA-MAN-MAN-MAN.29: 11 residues within 4Å: Chain I: N.361 Chain K: D.51, H.53, N.55, A.57, T.59, W.112, H.114 Chain L: D.94, K.97 Ligands: NAG-NAG.28 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain L Hydrogen bonds: K:D.51, L:K.97, L:K.97

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

NAG.31: 2 residues within 4Å: Chain A: N.107 Chain D: S.55 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: Q.100, S.120, N.122 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain A: E.62, N.204, T.206, G.207, P.208 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.271, I.292 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: V.2, N.26 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain E: N.107 Chain H: S.55 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: Q.100, S.120, N.122 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain E: E.62, N.204, T.206, G.207, P.208 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain E: N.271, I.292 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain E: N.308, W.364 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain G: V.2, N.26 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain I: N.107 Chain L: S.55 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain I: Q.100, S.120, N.122 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain I: E.62, N.204, T.206, G.207, P.208 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain I: N.271, I.292 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain I: N.308, W.364 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain K: V.2, N.26 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steichen, J.M. et al., A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses. Science (2019)

Release Date

2019-11-06

Peptides

Envelope glycoprotein gp160: AEI
Envelope glycoprotein gp160: BFJ
mature BG18 fragment antigen binding heavy chain: CGK
mature BG18 fragment antigen binding light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

I
D

B
B

F
E

J
F

C
H

G
G

K
I

D
L

H
J

L
K

Envelope glycoprotein gp160

Envelope glycoprotein gp160

mature BG18 fragment antigen binding heavy chain

mature BG18 fragment antigen binding light chain

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