SMTL ID : 9f02.1

HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with three copies of ELC07 broadly neutralizing antibody.

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: 8 residues within 4Å: Chain B: E.216, L.266, N.267, N.381, G.383, V.449, S.450 Ligands: NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.21: 7 residues within 4Å: Chain C: E.216, L.266, N.267, G.383, V.449, S.450 Ligands: NAG.40 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.23: 7 residues within 4Å: Chain L: E.216, L.266, N.267, G.383, V.449, S.450 Ligands: NAG.48 No protein-ligand interaction detected (PLIP)

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.2: 6 residues within 4Å: Chain B: E.92, N.93 Chain F: E.21, Q.23, G.46, R.97 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.23, F:G.46, F:R.97, F:R.97 NAG-NAG-BMA.22: 6 residues within 4Å: Chain C: E.92, N.93 Chain H: E.21, Q.23, G.46, R.97 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:Q.23, H:E.21, H:G.46, H:R.97, H:R.97 NAG-NAG-BMA.24: 7 residues within 4Å: Chain J: E.21, Q.23, Y.45, G.46, R.97 Chain L: E.92, N.93 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:Q.23, J:E.21, J:G.46, J:R.97, J:R.97

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.3: 3 residues within 4Å: Chain B: N.281, T.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain B: N.390, S.392 Ligands: NAG-NAG.5, NAG-NAG.5, NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain B: N.367, S.368, N.390, S.392 Ligands: NAG-NAG.4, NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: N.300, T.302, H.334, N.336, R.447 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.153, Y.170, D.325 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain B: Q.298, N.300, V.337, S.338, R.447 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.281, T.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain C: N.390, S.392 Ligands: NAG-NAG.11, NAG-NAG.11, NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain C: N.367, S.368, N.390, S.392 Ligands: NAG-NAG.10, NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.300, T.302, H.334, N.336, R.447 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.153, Y.170, D.325 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: Q.298, N.300, S.338, R.447 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain L: N.281, T.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain L: N.390, S.392 Ligands: NAG-NAG.17, NAG-NAG.17, NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain L: N.367, S.368, N.390, S.392 Ligands: NAG-NAG.16, NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain L: N.300, T.302, H.334, N.336, R.447 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain L: N.153, Y.170, D.325 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain L: Q.298, N.300, V.337, S.338 No protein-ligand interaction detected (PLIP)

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

NAG.25: 3 residues within 4Å: Chain B: N.239, S.279, H.356 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: S.392, N.396 Ligands: NAG-NAG.4 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.306, I.327, V.445 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.359 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: K.339, N.343, W.399 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: R.197, N.202, T.203 Chain C: R.313 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain B: N.267, L.270, P.296, N.451 Ligands: NAG-NAG-BMA-MAN.1 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.239, S.279, H.356 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: S.392, N.396 Ligands: NAG-NAG.10 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.306, I.327, V.445 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.359 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: K.339, N.343 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: R.197, N.202, T.203 Chain L: R.313 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain C: Q.135, S.155, F.156, N.157, K.168 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: K.257, N.267, P.296, N.451 Ligands: NAG-NAG-BMA-MAN.21 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain L: N.239, T.241, S.279, H.356 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain L: S.392, N.396 Ligands: NAG-NAG.16 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain L: N.306, I.327, V.445 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain L: N.359 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain L: K.339, N.343 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain B: R.313 Chain L: R.197, N.202, T.203 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain L: Q.135, S.155, F.156, N.157, K.168 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain L: K.257, N.267, P.296, N.451 Ligands: NAG-NAG-BMA-MAN.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Griffith, S. et al., TITLE: Preservation of memory B cell homeostasis in an individual producing broadly neutralizing antibodies against HIV-1. To Be Published

Release Date

2025-04-23

Peptides

Transmembrane protein gp41: ADE
Envelope glycoprotein gp160: BCL
ELC07 heavy chain: FHJ
ELC07 light chain: GIK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
F

E
E

B
C

C
G

L
N

F
H

H
I

J
K

G
L

I
J

K
M

Transmembrane protein gp41

Envelope glycoprotein gp160

ELC07 heavy chain

ELC07 light chain

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