- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.55 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.1: 6 residues within 4Å:- Chain A: N.142, T.144, I.180, S.182, L.185, H.244
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:L.185
- Hydrogen bonds: A:N.142
NAG.2: 2 residues within 4Å:- Chain A: N.137, N.149
No protein-ligand interaction detected (PLIP)NAG.3: 9 residues within 4Å:- Chain A: P.120, K.160, V.162, L.169, N.170, N.268, C.333, N.334, S.335
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:V.162, A:L.169
- Hydrogen bonds: A:K.160, A:N.170, A:S.335
NAG.4: 3 residues within 4Å:- Chain A: N.184, T.186, N.187
No protein-ligand interaction detected (PLIP)NAG.5: 6 residues within 4Å:- Chain A: E.176, E.177, I.178, N.197, K.236, E.240
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:I.178, A:N.197, A:E.240
NAG.6: 4 residues within 4Å:- Chain A: T.263, T.264, N.277, S.279
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:T.264
- Hydrogen bonds: A:N.277, A:S.279
- Water bridges: A:N.277
NAG.7: 7 residues within 4Å:- Chain A: E.253, P.254, D.280, N.283, T.294, G.295, R.296
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:P.254
- Hydrogen bonds: A:D.280, A:N.283, A:R.296
- 5 x SO4: SULFATE ION(Non-functional Binders)
SO4.8: 4 residues within 4Å:- Chain A: K.307, K.309, Q.310, I.311
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:Q.310, A:I.311
- Water bridges: A:K.307, A:K.309
- Salt bridges: A:K.307, A:K.309
SO4.9: 6 residues within 4Å:- Chain A: D.259, L.260, E.261, N.313
- Chain B: V.54, H.56
7 PLIP interactions:6 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:D.259, A:D.259, A:L.260, A:N.313
- Water bridges: A:K.309
- Salt bridges: A:K.309, B:H.56
SO4.10: 6 residues within 4Å:- Chain A: V.163, E.261, S.266, Y.275, W.315, M.365
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:S.266, B:Y.100
SO4.11: 5 residues within 4Å:- Chain A: T.186, N.188, R.344, G.346, G.347
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:D.345, A:G.347
- Water bridges: A:N.188
- Salt bridges: A:R.344
SO4.12: 4 residues within 4Å:- Chain B: V.2, Y.32, R.95, Y.110
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:Y.32, B:Y.32, B:Y.110
- Water bridges: B:R.95
- Salt bridges: B:R.95
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhou, T. et al., Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site. Structure (2022)
- Release Date
- 2022-03-30
- Peptides
- Glycoprotein 120: A
Lamma VHH antibody J3: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.55 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 5 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhou, T. et al., Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site. Structure (2022)
- Release Date
- 2022-03-30
- Peptides
- Glycoprotein 120: A
Lamma VHH antibody J3: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B