SMTL ID : 7rso.1

AMC016 SOSIP.v4.2 in complex with PGV04 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

24 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: 7 residues within 4Å: Chain A: L.105, N.135, Y.152, T.154, G.298, Q.299, I.300 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.152 NAG-NAG.2: 4 residues within 4Å: Chain A: N.213, T.215, S.253 Ligands: NAG.39 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.241, S.270, N.421 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain A: R.313, N.317, W.372, E.376, S.377, S.378 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: M.350, N.363, T.365 Ligands: NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: N.101, D.166, N.168, S.169 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: E.272, I.273, N.274, S.419, S.420 Ligands: NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain A: T.276, N.310, N.386, T.388 Ligands: NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 7 residues within 4Å: Chain E: L.105, N.135, Y.152, T.154, G.298, Q.299, I.300 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.152 NAG-NAG.14: 4 residues within 4Å: Chain E: N.213, T.215, S.253 Ligands: NAG.54 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain E: N.241, S.270, N.421 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.16 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain E: R.313, N.317, W.372, E.376, S.377, S.378 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain E: M.350, N.363, T.365 Ligands: NAG.57 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain E: N.101, D.166, N.168, S.169 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 6 residues within 4Å: Chain E: E.272, I.273, N.274, S.419, S.420 Ligands: NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain E: T.276, N.310, N.386, T.388 Ligands: NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 7 residues within 4Å: Chain G: L.105, N.135, Y.152, T.154, G.298, Q.299, I.300 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.152 NAG-NAG.26: 4 residues within 4Å: Chain G: N.213, T.215, S.253 Ligands: NAG.69 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain G: N.241, S.270, N.421 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.28 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 6 residues within 4Å: Chain G: R.313, N.317, W.372, E.376, S.377, S.378 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain G: M.350, N.363, T.365 Ligands: NAG.72 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain G: N.101, D.166, N.168, S.169 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 6 residues within 4Å: Chain G: E.272, I.273, N.274, S.419, S.420 Ligands: NAG-NAG-BMA.35 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 5 residues within 4Å: Chain G: T.276, N.310, N.386, T.388 Ligands: NAG-NAG-BMA.35 No protein-ligand interaction detected (PLIP)

6 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.3: 6 residues within 4Å: Chain A: E.54, V.56, N.208, N.220, S.222 Ligands: NAG.39 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.54, A:V.56 NAG-NAG-BMA.11: 7 residues within 4Å: Chain A: N.310, E.384, G.385, N.386 Ligands: NAG-NAG.10, NAG-NAG.12, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 6 residues within 4Å: Chain E: E.54, V.56, N.208, N.220, S.222 Ligands: NAG.54 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.54, E:V.56 NAG-NAG-BMA.23: 7 residues within 4Å: Chain E: N.310, E.384, G.385, N.386 Ligands: NAG-NAG.22, NAG-NAG.24, NAG-NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 6 residues within 4Å: Chain G: E.54, V.56, N.208, N.220, S.222 Ligands: NAG.69 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:E.54, G:V.56 NAG-NAG-BMA.35: 7 residues within 4Å: Chain G: N.310, E.384, G.385, N.386 Ligands: NAG-NAG.34, NAG-NAG.36, NAG-NAG.36 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: 13 residues within 4Å: Chain A: R.37, P.185, P.191, V.233, L.240, N.241, R.283, N.354, G.356, C.418, S.419, S.420 Ligands: NAG-NAG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.419 NAG-NAG-BMA-MAN-MAN-MAN.16: 13 residues within 4Å: Chain E: R.37, P.185, P.191, V.233, L.240, N.241, R.283, N.354, G.356, C.418, S.419, S.420 Ligands: NAG-NAG.18 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.419 NAG-NAG-BMA-MAN-MAN-MAN.28: 13 residues within 4Å: Chain G: R.37, P.185, P.191, V.233, L.240, N.241, R.283, N.354, G.356, C.418, S.419, S.420 Ligands: NAG-NAG.30 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.419

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.5: 7 residues within 4Å: Chain A: N.255 Chain C: G.107, Q.108, G.109 Chain D: G.29, H.30, G.66 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 7 residues within 4Å: Chain E: N.255 Chain I: G.107, Q.108, G.109 Chain J: G.29, H.30, G.66 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.29: 7 residues within 4Å: Chain G: N.255 Chain K: G.107, Q.108, G.109 Chain L: G.29, H.30, G.66 No protein-ligand interaction detected (PLIP)

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

NAG.37: 4 residues within 4Å: Chain A: I.163, R.171, N.176 Chain G: V.144 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain A: A.58, N.59 Chain B: G.17, S.18 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain A: N.209, N.220 Ligands: NAG-NAG.2, NAG-NAG-BMA.3 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain A: L.105, G.302, N.303, I.304 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain A: N.333 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain A: T.365, Q.366, N.369 Ligands: NAG-NAG.8, NAG-NAG.8 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain A: N.280, I.301, Q.415 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain A: Y.373, G.374, N.375 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain A: E.247, E.248, N.268, E.269 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: N.165, D.166, N.167 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain A: N.139, M.148 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain A: N.435 Chain D: E.1, I.2 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain B: N.101, S.103, W.104 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain B: K.123, E.124, S.126, N.127 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain B: N.111, N.115 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain A: V.144 Chain E: I.163, R.171, N.176 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain E: A.58, N.59 Chain F: G.17, S.18 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain E: N.209, N.220 Ligands: NAG-NAG.14, NAG-NAG-BMA.15 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain E: L.105, G.302, N.303, I.304 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain E: N.333 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain E: T.365, Q.366, N.369 Ligands: NAG-NAG.20, NAG-NAG.20 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain E: N.280, I.301, Q.415 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain E: Y.373, G.374, N.375 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain E: E.247, E.248, N.268, E.269 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain E: N.165, D.166, N.167 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain E: N.139, M.148 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain E: N.435 Chain J: E.1, I.2 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain F: N.101, S.103, W.104 Ligand excluded by PLIP NAG.65: 4 residues within 4Å: Chain F: K.123, E.124, S.126, N.127 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain F: N.111, N.115 Ligand excluded by PLIP NAG.67: 4 residues within 4Å: Chain E: V.144 Chain G: I.163, R.171, N.176 Ligand excluded by PLIP NAG.68: 4 residues within 4Å: Chain G: A.58, N.59 Chain H: G.17, S.18 Ligand excluded by PLIP NAG.69: 4 residues within 4Å: Chain G: N.209, N.220 Ligands: NAG-NAG.26, NAG-NAG-BMA.27 Ligand excluded by PLIP NAG.70: 4 residues within 4Å: Chain G: L.105, G.302, N.303, I.304 Ligand excluded by PLIP NAG.71: 1 residues within 4Å: Chain G: N.333 Ligand excluded by PLIP NAG.72: 5 residues within 4Å: Chain G: T.365, Q.366, N.369 Ligands: NAG-NAG.32, NAG-NAG.32 Ligand excluded by PLIP NAG.73: 3 residues within 4Å: Chain G: N.280, I.301, Q.415 Ligand excluded by PLIP NAG.74: 3 residues within 4Å: Chain G: Y.373, G.374, N.375 Ligand excluded by PLIP NAG.75: 4 residues within 4Å: Chain G: E.247, E.248, N.268, E.269 Ligand excluded by PLIP NAG.76: 3 residues within 4Å: Chain G: N.165, D.166, N.167 Ligand excluded by PLIP NAG.77: 2 residues within 4Å: Chain G: N.139, M.148 Ligand excluded by PLIP NAG.78: 3 residues within 4Å: Chain G: N.435 Chain L: E.1, I.2 Ligand excluded by PLIP NAG.79: 3 residues within 4Å: Chain H: N.101, S.103, W.104 Ligand excluded by PLIP NAG.80: 4 residues within 4Å: Chain H: K.123, E.124, S.126, N.127 Ligand excluded by PLIP NAG.81: 2 residues within 4Å: Chain H: N.111, N.115 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schorcht, A. et al., The Glycan Hole Area of HIV-1 Envelope Trimers Contributes Prominently to the Induction of Autologous Neutralization. J.Virol. (2022)

Release Date

2021-09-15

Peptides

AMC016 gp120: AEG
AMC016 gp41: BFH
PGV04 Fab heavy chain: CIK
PGV04 kappa chain: DJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

G
D

B
B

F
E

H
F

C
H

I
G

K
I

D
L

J
J

L
K

AMC016 gp120

AMC016 gp41

PGV04 Fab heavy chain

PGV04 kappa chain

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