SMTL ID : 6x9v.1 (2 other biounits)

HIV-1 Envelope Glycoprotein BG505 SOSIP.664, expressed in HEK293S cells and deglycosylated by endoglycosidase H, in complex with RM20A3 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

12 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: V.139, N.141, N.153, Y.170, D.325 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.170 NAG-NAG.2: 5 residues within 4Å: Chain A: V.179, R.197, I.199, N.202, T.203 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.199 NAG-NAG.4: 4 residues within 4Å: Chain A: N.390, S.392 Ligands: NAG.17, NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: P.296, V.449, S.450, N.451 Ligands: NAG-NAG-BMA-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain E: V.139, N.141, N.153, Y.170, D.325 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.170 NAG-NAG.24: 5 residues within 4Å: Chain E: V.179, R.197, I.199, N.202, T.203 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.199 NAG-NAG.26: 4 residues within 4Å: Chain E: N.390, S.392 Ligands: NAG.39, NAG.40 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain E: P.296, V.449, S.450, N.451 Ligands: NAG-NAG-BMA-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 5 residues within 4Å: Chain I: V.139, N.141, N.153, Y.170, D.325 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.170 NAG-NAG.46: 5 residues within 4Å: Chain I: V.179, R.197, I.199, N.202, T.203 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:I.199 NAG-NAG.48: 4 residues within 4Å: Chain I: N.390, S.392 Ligands: NAG.61, NAG.62 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 5 residues within 4Å: Chain I: P.296, V.449, S.450, N.451 Ligands: NAG-NAG-BMA-MAN.47 No protein-ligand interaction detected (PLIP)

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.3: 9 residues within 4Å: Chain A: S.214, P.217, L.266, N.267, C.382, G.383, V.449, S.450 Ligands: NAG-NAG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.383, A:S.214, A:S.214 NAG-NAG-BMA-MAN.25: 9 residues within 4Å: Chain E: S.214, P.217, L.266, N.267, C.382, G.383, V.449, S.450 Ligands: NAG-NAG.27 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.383, E:S.214, E:S.214 NAG-NAG-BMA-MAN.47: 9 residues within 4Å: Chain I: S.214, P.217, L.266, N.267, C.382, G.383, V.449, S.450 Ligands: NAG-NAG.49 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:G.383, I:S.214, I:S.214

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

NAG.6: 3 residues within 4Å: Chain A: E.92, N.93 Chain B: S.17 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: T.137, N.138, G.149 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.141, N.142 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.10: 5 residues within 4Å: Chain A: N.239, T.241, S.279, I.282, H.356 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.281, T.283, N.284 Ligand excluded by PLIP NAG.12: 6 residues within 4Å: Chain A: Q.298, N.300, N.336, V.337, S.338, R.447 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.306, V.445 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: N.300, T.302, H.334, N.336, T.418 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.343, I.400 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.359 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.367, S.368, T.376 Ligands: NAG-NAG.4 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: S.392, N.396 Ligands: NAG-NAG.4, NAG-NAG.4 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: P.98, N.100, S.102 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: R.106, N.107, E.110 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.114 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain E: E.92, N.93 Chain F: S.17 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain E: T.137, N.138, G.149 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain E: N.141, N.142 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain E: Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain E: N.239, T.241, S.279, I.282, H.356 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain E: N.281, T.283, N.284 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain E: Q.298, N.300, N.336, V.337, S.338, R.447 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain E: N.306, V.445 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain E: N.300, T.302, H.334, N.336, T.418 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain E: N.343, I.400 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain E: N.359 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain E: N.367, S.368, T.376 Ligands: NAG-NAG.26 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain E: S.392, N.396 Ligands: NAG-NAG.26, NAG-NAG.26 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain F: P.98, N.100, S.102 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain F: R.106, N.107, E.110 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain F: N.114 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain F: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain I: E.92, N.93 Chain J: S.17 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain I: T.137, N.138, G.149 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain I: N.141, N.142 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain I: Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain I: N.239, T.241, S.279, I.282, H.356 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain I: N.281, T.283, N.284 Ligand excluded by PLIP NAG.56: 6 residues within 4Å: Chain I: Q.298, N.300, N.336, V.337, S.338, R.447 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain I: N.306, V.445 Ligand excluded by PLIP NAG.58: 5 residues within 4Å: Chain I: N.300, T.302, H.334, N.336, T.418 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain I: N.343, I.400 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain I: N.359 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain I: N.367, S.368, T.376 Ligands: NAG-NAG.48 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain I: S.392, N.396 Ligands: NAG-NAG.48, NAG-NAG.48 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain J: P.98, N.100, S.102 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain J: R.106, N.107, E.110 Ligand excluded by PLIP NAG.65: 1 residues within 4Å: Chain J: N.114 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain J: E.123, N.126, Y.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berndsen, Z.T. et al., Visualization of the HIV-1 Env glycan shield across scales. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-11-04

Peptides

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120: AEI
HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41: BFJ
RM20A3 Fab Heavy Chain: CGK
RM20A3 Fab Light Chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
H

G
H

K
H

D
L

H
L

L
L

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41

RM20A3 Fab Heavy Chain

RM20A3 Fab Light Chain

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