SMTL ID : 6dfh.1

BG505 MD64 N332-GT2 SOSIP trimer in complex with germline-reverted BG18 fragment antigen binding

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 3 residues within 4Å: Chain A: Y.104, N.118, Y.135 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.135 NAG-NAG.2: 3 residues within 4Å: Chain A: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: T.341, N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.204, E.245 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: P.261, Q.263, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain E: Y.104, N.118, Y.135 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.135 NAG-NAG.10: 3 residues within 4Å: Chain E: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain E: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain E: T.341, N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain E: N.204, E.245 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain I: Y.104, N.118, Y.135 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.135 NAG-NAG.18: 3 residues within 4Å: Chain I: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain I: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain I: T.341, N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain I: N.204, E.245 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain I: P.261, Q.263, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.22 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: 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.6: 8 residues within 4Å: Chain A: E.34, N.232, N.346, C.347, Q.408, V.414, S.415 Ligands: NAG-NAG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.347, A:V.414, A:Q.408 NAG-NAG-BMA-MAN-MAN.14: 8 residues within 4Å: Chain E: E.34, N.232, N.346, C.347, Q.408, V.414, S.415 Ligands: NAG-NAG.16 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:C.347, E:V.414, E:Q.408 NAG-NAG-BMA-MAN-MAN.22: 8 residues within 4Å: Chain I: E.34, N.232, N.346, C.347, Q.408, V.414, S.415 Ligands: NAG-NAG.24 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:C.347, I:V.414, I:Q.408

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.7: 13 residues within 4Å: Chain A: T.267, R.296, H.299, N.301, S.381, I.383 Chain C: T.102, I.103, F.104, G.105, V.106, V.107, Y.113 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN.15: 13 residues within 4Å: Chain E: T.267, R.296, H.299, N.301, S.381, I.383 Chain G: T.102, I.103, F.104, G.105, V.106, V.107, Y.113 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN.23: 13 residues within 4Å: Chain I: T.267, R.296, H.299, N.301, S.381, I.383 Chain K: T.102, I.103, F.104, G.105, V.106, V.107, Y.113 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:V.107

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

NAG.25: 6 residues within 4Å: Chain A: T.98, Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.271, L.292 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: V.144, R.162, N.167 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.308 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.361 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain E: T.98, Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain E: N.271, L.292 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain E: V.144, R.162, N.167 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain E: N.361 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain I: T.98, Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain I: N.271, L.292 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain I: V.144, R.162, N.167 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain I: N.308 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain I: N.361 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain J: N.100, S.102 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
germline-reverted BG18 fragment antigen binding heavy chain: CGK
germline-reverted 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

germline-reverted BG18 fragment antigen binding heavy chain

germline-reverted BG18 fragment antigen binding light chain