- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-3-3-1-3-1-3-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: 3 residues within 4Å:- Chain A: E.55, N.56
- Chain B: S.17
No protein-ligand interaction detected (PLIP)NAG-NAG.4: 3 residues within 4Å:- Chain A: V.142, R.160, N.165
No protein-ligand interaction detected (PLIP)NAG-NAG.5: 4 residues within 4Å:- Chain A: N.202, T.204, S.242, H.319
No protein-ligand interaction detected (PLIP)NAG-NAG.7: 5 residues within 4Å:- Chain A: N.244
- Chain L: D.28, V.29, G.30, W.31
No protein-ligand interaction detected (PLIP)NAG-NAG.8: 6 residues within 4Å:- Chain A: N.263, N.299, V.300, S.301, S.379, R.410
No protein-ligand interaction detected (PLIP)NAG-NAG.9: 2 residues within 4Å:- Chain A: N.269, I.290
No protein-ligand interaction detected (PLIP)NAG-NAG.10: 4 residues within 4Å:- Chain A: T.265, H.297, N.299, R.410
No protein-ligand interaction detected (PLIP)NAG-NAG.11: 6 residues within 4Å:- Chain A: N.330, T.339, N.353, S.355
- Ligands: NAG-NAG.12, NAG-NAG.12
No protein-ligand interaction detected (PLIP)NAG-NAG.12: 4 residues within 4Å:- Chain A: N.353, S.355
- Ligands: NAG-NAG.11, NAG-NAG.11
No protein-ligand interaction detected (PLIP)NAG-NAG.13: 4 residues within 4Å:- Chain C: V.102, N.116, Y.133, D.288
No protein-ligand interaction detected (PLIP)NAG-NAG.15: 2 residues within 4Å:- Chain C: N.202
- Ligands: NAG-NAG.16
No protein-ligand interaction detected (PLIP)NAG-NAG.16: 7 residues within 4Å:- Chain C: E.243, N.244
- Chain J: D.115
- Chain N: V.29, W.31, T.50
- Ligands: NAG-NAG.15
1 PLIP interactions:1 interactions with chain N- Hydrophobic interactions: N:T.50
NAG-NAG.17: 4 residues within 4Å:- Chain C: N.263, N.299, S.301, R.410
No protein-ligand interaction detected (PLIP)NAG-NAG.18: 2 residues within 4Å:- Chain C: N.269, I.290
No protein-ligand interaction detected (PLIP)NAG-NAG.19: 6 residues within 4Å:- Chain C: N.263, T.265, H.297, N.299, T.381, R.410
No protein-ligand interaction detected (PLIP)NAG-NAG.21: 4 residues within 4Å:- Chain C: N.353, S.355
- Ligands: NAG-NAG-BMA.20, NAG-NAG-BMA.20
No protein-ligand interaction detected (PLIP)NAG-NAG.27: 2 residues within 4Å:- Chain E: N.202, T.204
No protein-ligand interaction detected (PLIP)NAG-NAG.29: 7 residues within 4Å:- Chain E: N.244
- Chain I: D.115
- Chain M: D.28, V.29, G.30, W.31, T.50
3 PLIP interactions:3 interactions with chain M- Hydrophobic interactions: M:W.31, M:T.50
- Hydrogen bonds: M:W.31
NAG-NAG.30: 6 residues within 4Å:- Chain E: Q.261, N.263, V.300, S.301, R.410, V.412
No protein-ligand interaction detected (PLIP)NAG-NAG.31: 1 residues within 4Å:- Chain E: N.269
No protein-ligand interaction detected (PLIP)NAG-NAG.32: 4 residues within 4Å:- Chain E: T.265, H.297, N.299, R.410
No protein-ligand interaction detected (PLIP)NAG-NAG.33: 5 residues within 4Å:- Chain E: N.330, S.331, T.339
- Ligands: NAG-NAG.34, NAG-NAG.34
No protein-ligand interaction detected (PLIP)NAG-NAG.34: 4 residues within 4Å:- Chain E: N.353, S.355
- Ligands: NAG-NAG.33, NAG-NAG.33
No protein-ligand interaction detected (PLIP)NAG-NAG.35: 4 residues within 4Å:- Chain E: P.259, Q.261, N.414
- Ligands: NAG-NAG-BMA-MAN.28
No protein-ligand interaction detected (PLIP)- 5 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: 4 residues within 4Å:- Chain A: V.102, N.116, Y.133, L.135
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.20: 4 residues within 4Å:- Chain C: N.330, N.353
- Ligands: NAG-NAG.21, NAG-NAG.21
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.23: 6 residues within 4Å:- Chain C: R.160, N.165
- Chain E: R.276
- Chain J: R.19, D.84, S.86
1 PLIP interactions:1 interactions with chain J- Hydrogen bonds: J:R.19
NAG-NAG-BMA.24: 4 residues within 4Å:- Chain E: V.102, N.116, Y.133, D.288
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.26: 5 residues within 4Å:- Chain E: V.142, R.160, N.165
- Chain I: R.19, S.86
1 PLIP interactions:1 interactions with chain I- Hydrogen bonds: I:R.19
- 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.3: 7 residues within 4Å:- Chain A: T.96, S.118, F.119, N.120
- Chain K: G.55, D.56, K.58
1 PLIP interactions:1 interactions with chain K- Hydrogen bonds: K:D.56
NAG-NAG-BMA-MAN-MAN.6: 11 residues within 4Å:- Chain A: K.33, P.180, V.222, L.229, N.230, N.344, G.346, C.411, V.412, S.413
- Ligands: NAG.37
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA-MAN-MAN.22: 7 residues within 4Å:- Chain C: E.179, L.229, N.230, N.344, V.412, S.413
- Ligands: NAG.40
No protein-ligand interaction detected (PLIP)- 1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN.14: 15 residues within 4Å:- Chain C: T.96, Q.98, S.118, F.119, N.120
- Chain G: H.31, G.32, R.97, S.99
- Chain K: D.106, Y.107, W.118, V.120, V.122, Y.124
2 PLIP interactions:1 interactions with chain K, 1 interactions with chain C- Hydrophobic interactions: K:V.120
- Hydrogen bonds: C:Q.98
- 1 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.25: 15 residues within 4Å:- Chain A: D.127
- Chain E: T.96, Q.98, N.120
- Chain G: N.35, Y.37
- Chain K: T.31, Y.32, H.53, S.100, K.101, H.102, R.103, L.104, Y.110
5 PLIP interactions:2 interactions with chain K, 3 interactions with chain G- Hydrophobic interactions: K:L.104
- Hydrogen bonds: K:R.103, K:R.103, G:N.35, G:Y.37, G:Y.37
- 1 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.28: 9 residues within 4Å:- Chain E: E.179, P.180, K.220, L.229, N.230, G.346, V.412, S.413
- Ligands: NAG-NAG.35
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:E.179, E:E.179
- 7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.36: 1 residues within 4Å:- Chain A: N.306
No protein-ligand interaction detected (PLIP)NAG.37: 3 residues within 4Å:- Chain A: P.259, N.414
- Ligands: NAG-NAG-BMA-MAN-MAN.6
No protein-ligand interaction detected (PLIP)NAG.38: 3 residues within 4Å:- Chain C: E.55, N.56
- Chain D: S.17
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:E.55
NAG.39: 3 residues within 4Å:- Chain C: K.302, N.306, W.362
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:K.302
NAG.40: 3 residues within 4Å:- Chain C: P.259, N.414
- Ligands: NAG-NAG-BMA-MAN-MAN.22
No protein-ligand interaction detected (PLIP)NAG.41: 3 residues within 4Å:- Chain E: E.55, N.56
- Chain F: S.17
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:E.55
- Hydrogen bonds: E:N.56
NAG.42: 2 residues within 4Å:- Chain E: N.306, W.362
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gieselmann, L. et al., Profiling of HIV-1 elite neutralizer cohort reveals a CD4bs bnAb for HIV-1 prevention and therapy. Nat.Immunol. (2025)
- Release Date
- 2025-04-16
- Peptides
- Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF
PGDM1400 Fab Light Chain: G
04_A06 Fab Heavy Chain: HIJ
PGDM1400 Fab Heavy Chain: K
04_A06 Fab Light Chain: LMN - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
CE
EB
BD
DF
FG
GH
HI
IJ
JK
KL
LM
MN
N
SMTL ID : 8ulu.1
Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 04_A06 and PGDM1400 Fabs
Envelope glycoprotein gp120
Toggle Identical (ACE)Envelope glycoprotein gp41
Toggle Identical (BDF)PGDM1400 Fab Light Chain
04_A06 Fab Heavy Chain
Toggle Identical (HIJ)PGDM1400 Fab Heavy Chain
04_A06 Fab Light Chain
Toggle Identical (LMN)Related Entries With Identical Sequence
4rqq.1 | 4rqq.2 | 4rqq.3 | 4tvp.1 | 4zmj.1 | 5aco.1 | 5c7k.1 | 5cez.2 | 5cjx.1 | 5fyl.1 | 5t3x.1 | 5t3z.1 | 5thr.1 | 5u7m.1 | 5u7o.1 | 5utf.1 | 5uty.1 | 5v7j.1 | 5v8l.1 | 5v8m.1 | 5viy.1 | 5vj6.1 | 5w6d.1 | 6cm3.1 | 6crq.1 | 6de7.1 | 6did.1 | 6mn7.1 | 6mtj.1 | 6mtn.1 more...less...6mu6.1 | 6mu7.1 | 6mu8.1 | 6nf2.1 | 6nm6.1 | 6nnf.1 | 6nnj.1 | 6opa.1 | 6osy.1 | 6ot1.1 | 6oz4.1 | 6ozc.1 | 6pw6.1 | 6u0l.1 | 6u0n.1 | 6udj.1 | 6vi0.1 | 6vn0.1 | 6w03.1 | 6x96.1 | 6x97.1 | 6x98.1 | 6x9r.1 | 6x9r.2 | 6x9r.3 | 6x9s.1 | 6x9s.2 | 6x9s.3 | 6x9t.1 | 6x9t.2 | 6x9t.3 | 6x9u.1 | 6x9u.2 | 6x9u.3 | 6x9v.1 | 6x9v.2 | 6x9v.3 | 6xrt.1 | 7kde.1 | 7lo6.1 | 7lok.1 | 7lpn.1 | 7mxe.1 | 7pc2.1 | 7rai.1 | 7tfn.1 | 7tfo.1 | 7txd.1 | 7ucf.1 | 7uoj.1 | 8dp1.1 | 8dto.1 | 8e1p.1 | 8euu.1 | 8euv.1 | 8euw.1 | 8fis.1 | 8fk5.1 | 8fl1.1 | 8flw.1 | 8fyj.1 | 8g85.1 | 8g9w.1 | 8g9x.1 | 8g9y.1 | 8gas.1 | 8jtd.1 | 8jtm.1 | 8sal.1 | 8san.1 | 8saq.1 | 8sat.1 | 8sav.1 | 8sw3.1 | 8sw4.1 | 8tjr.1 | 8tjs.1 | 8tkc.1 | 8tl2.1 | 8tl3.1 | 8tl4.1 | 8tl5.1 | 8tng.1 | 8tnh.1 | 8tni.1 | 8tnu.1 | 8to7.1 | 8top.1 | 8tq1.1 | 8ttw.1 | 8uki.1 | 8ulr.1 | 8uls.1 | 8ult.1 | 9aug.1 | 9auh.1 | 9aui.1 | 9cf5.1 | 9d1w.1 | 9d3d.1 | 9d8y.1 | 9d98.1 | 9dmb.1 | 9ehl.1 | 9ehm.1 | 9mi0.1 | 9mia.1 | 9mib.1 | 9mih.1 | 9mii.1