- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-3-3-3-3-mer
- Ligands
- 1 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.1: 10 residues within 4Å:- Chain A: K.222, V.224, L.231, N.232, N.346, C.347, G.348, C.413, V.414, S.415
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:G.348
- 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.2: 1 residues within 4Å:- Chain A: N.265
No protein-ligand interaction detected (PLIP)NAG-NAG.3: 5 residues within 4Å:- Chain A: T.267, H.299, N.301, S.381, T.383
No protein-ligand interaction detected (PLIP)NAG-NAG.4: 6 residues within 4Å:- Chain A: N.332, T.341, N.355, S.357
- Ligands: NAG-NAG.5, NAG-NAG.5
No protein-ligand interaction detected (PLIP)NAG-NAG.5: 5 residues within 4Å:- Chain A: N.355, S.357
- Ligands: NAG-NAG.4, NAG-NAG.4, NAG.30
No protein-ligand interaction detected (PLIP)NAG-NAG.8: 3 residues within 4Å:- Chain C: E.57, N.58
- Chain D: S.17
No protein-ligand interaction detected (PLIP)NAG-NAG.10: 4 residues within 4Å:- Chain C: Q.263, N.265, S.303, R.412
No protein-ligand interaction detected (PLIP)NAG-NAG.11: 6 residues within 4Å:- Chain C: T.267, H.299, N.301, S.381, T.383, R.412
No protein-ligand interaction detected (PLIP)NAG-NAG.12: 8 residues within 4Å:- Chain C: N.332, S.333, G.335, T.341, S.357
- Ligands: NAG-NAG.13, NAG-NAG.13, NAG.42
No protein-ligand interaction detected (PLIP)NAG-NAG.13: 6 residues within 4Å:- Chain C: N.355, S.357, R.387
- Ligands: NAG-NAG.12, NAG-NAG.12, NAG.42
No protein-ligand interaction detected (PLIP)NAG-NAG.17: 3 residues within 4Å:- Chain E: Q.263, N.265, R.412
No protein-ligand interaction detected (PLIP)NAG-NAG.18: 5 residues within 4Å:- Chain E: T.267, H.299, N.301, S.381, T.383
No protein-ligand interaction detected (PLIP)NAG-NAG.19: 7 residues within 4Å:- Chain E: N.332, S.333, G.335, T.341
- Ligands: NAG-NAG-BMA.20, NAG-NAG-BMA.20, NAG.54
No protein-ligand interaction detected (PLIP)- 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.6: 2 residues within 4Å:- Chain A: P.261, N.416
1 PLIP interactions:1 interactions with chain K- Hydrogen bonds: K:Q.3
- 2 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.7: 3 residues within 4Å:- Chain A: E.57, N.58
- Chain B: S.17
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA-MAN-MAN.16: 6 residues within 4Å:- Chain E: N.232, C.347, G.348, I.407, V.414, S.415
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:G.348
- 1 x NAG- NAG- BMA- MAN: 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.9: 6 residues within 4Å:- Chain C: E.181, N.232, C.347, V.414, S.415
- Ligands: NAG-NAG-BMA.14
No protein-ligand interaction detected (PLIP)- 4 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.14: 4 residues within 4Å:- Chain C: N.232, P.261, N.416
- Ligands: NAG-NAG-BMA-MAN.9
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.15: 8 residues within 4Å:- Chain E: E.57, N.58
- Chain F: G.16, S.17
- Chain H: T.31, Y.49, W.50, T.53
1 PLIP interactions:1 interactions with chain H- Hydrogen bonds: H:T.31
- Hydrophobic interactions: H:T.53
NAG-NAG-BMA.20: 5 residues within 4Å:- Chain E: N.355, S.357
- Ligands: NAG-NAG.19, NAG-NAG.19, NAG.54
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.21: 2 residues within 4Å:- Chain E: P.261, N.416
No protein-ligand interaction detected (PLIP)- 35 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.22: 1 residues within 4Å:- Chain A: N.103
Ligand excluded by PLIPNAG.23: 4 residues within 4Å:- Chain A: V.104, N.106, N.118, D.290
Ligand excluded by PLIPNAG.24: 4 residues within 4Å:- Chain A: T.98, Q.100, N.122
- Chain E: D.129
Ligand excluded by PLIPNAG.25: 2 residues within 4Å:- Chain A: R.162, N.167
Ligand excluded by PLIPNAG.26: 3 residues within 4Å:- Chain A: N.246, T.248, N.249
Ligand excluded by PLIPNAG.27: 3 residues within 4Å:- Chain A: N.271, I.292, V.410
Ligand excluded by PLIPNAG.28: 1 residues within 4Å:- Chain A: N.324
Ligand excluded by PLIPNAG.29: 2 residues within 4Å:- Chain A: N.308, W.364
Ligand excluded by PLIPNAG.30: 2 residues within 4Å:- Chain A: N.361
- Ligands: NAG-NAG.5
Ligand excluded by PLIPNAG.31: 2 residues within 4Å:- Chain A: N.204, T.206
Ligand excluded by PLIPNAG.32: 1 residues within 4Å:- Chain B: N.100
Ligand excluded by PLIPNAG.33: 2 residues within 4Å:- Chain B: N.126, Y.127
Ligand excluded by PLIPNAG.34: 2 residues within 4Å:- Chain C: N.103, K.117
Ligand excluded by PLIPNAG.35: 3 residues within 4Å:- Chain C: V.104, N.118, L.137
Ligand excluded by PLIPNAG.36: 2 residues within 4Å:- Chain C: S.120, N.122
Ligand excluded by PLIPNAG.37: 3 residues within 4Å:- Chain C: R.162, N.167, T.168
Ligand excluded by PLIPNAG.38: 3 residues within 4Å:- Chain C: N.246, T.248, N.249
Ligand excluded by PLIPNAG.39: 3 residues within 4Å:- Chain C: N.271, I.292, V.410
Ligand excluded by PLIPNAG.40: 1 residues within 4Å:- Chain C: N.324
Ligand excluded by PLIPNAG.41: 2 residues within 4Å:- Chain C: N.308, W.364
Ligand excluded by PLIPNAG.42: 3 residues within 4Å:- Chain C: N.361
- Ligands: NAG-NAG.12, NAG-NAG.13
Ligand excluded by PLIPNAG.43: 3 residues within 4Å:- Chain C: N.204, T.206, S.244
Ligand excluded by PLIPNAG.44: 2 residues within 4Å:- Chain D: P.98, N.100
Ligand excluded by PLIPNAG.45: 3 residues within 4Å:- Chain D: N.126
- Chain K: T.71, R.72
Ligand excluded by PLIPNAG.46: 2 residues within 4Å:- Chain E: N.103, G.114
Ligand excluded by PLIPNAG.47: 2 residues within 4Å:- Chain E: V.104, N.118
Ligand excluded by PLIPNAG.48: 2 residues within 4Å:- Chain E: Q.100, N.122
Ligand excluded by PLIPNAG.49: 1 residues within 4Å:- Chain E: N.167
Ligand excluded by PLIPNAG.50: 3 residues within 4Å:- Chain E: N.246, T.248, N.249
Ligand excluded by PLIPNAG.51: 3 residues within 4Å:- Chain E: N.271, I.292, V.410
Ligand excluded by PLIPNAG.52: 1 residues within 4Å:- Chain E: N.324
Ligand excluded by PLIPNAG.53: 2 residues within 4Å:- Chain E: N.308, W.364
Ligand excluded by PLIPNAG.54: 3 residues within 4Å:- Chain E: N.361
- Ligands: NAG-NAG.19, NAG-NAG-BMA.20
Ligand excluded by PLIPNAG.55: 3 residues within 4Å:- Chain E: N.204, T.206, S.244
Ligand excluded by PLIPNAG.56: 3 residues within 4Å:- Chain F: N.126, Y.127
- Chain I: R.72
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Sastry, M. et al., Diverse Murine Vaccinations Reveal Distinct Antibody Classes to Target Fusion Peptide and Variation in Peptide Length to Improve HIV Neutralization. J.Virol. (2023)
- Release Date
- 2023-04-19
- Peptides
- Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF
vFP52.02 Heavy: GIK
vFP52.02 Light: HJL - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
GC
DE
JB
BD
EF
KG
HI
AK
FH
LJ
CL
I
SMTL ID : 8g85.1
vFP52.02 Fab in complex with BG505 DS-SOSIP Env trimer
Envelope glycoprotein gp120
Toggle Identical (ACE)Envelope glycoprotein gp41
Toggle Identical (BDF)vFP52.02 Heavy
Toggle Identical (GIK)vFP52.02 Light
Toggle Identical (HJL)Related Entries With Identical Sequence
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 | 6mu6.1 | 6mu7.1 | 6mu8.1 more...less...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 | 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