SMTL ID : 8tjs.1

CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO GPZ6-a.01 FAB

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 14 residues within 4Å: Chain A: K.35, S.179, E.181, V.224, L.231, N.232, F.345, N.346, G.348, Q.408, C.413, V.414, S.415 Ligands: NAG.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN-MAN-MAN.4: 12 residues within 4Å: Chain C: K.35, P.176, S.179, E.181, N.232, R.274, F.345, N.346, G.348, V.414, S.415 Ligands: NAG.33 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.348 NAG-NAG-BMA-MAN-MAN-MAN.7: 12 residues within 4Å: Chain E: K.35, S.179, E.181, L.231, N.232, N.346, G.348, Q.408, C.413, V.414, S.415 Ligands: NAG.49 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.348

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.2: 5 residues within 4Å: Chain A: V.144, R.162, I.164, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: V.144, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain C: T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain C: R.278 Chain E: V.144, R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain E: T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP)

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

NAG.10: 3 residues within 4Å: Chain A: N.204, T.206, S.244 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.246, T.248 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: N.332, S.333, T.341 Ligands: NAG.15, NAG.16 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: T.342, N.355 Ligands: NAG.14 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG.14 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: V.104, N.106, N.118, S.120, D.290 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: Q.100, S.120, N.122 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.271, I.292, V.410 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: E.57, N.58 Chain B: S.17 Chain I: Y.107 Ligand excluded by PLIP NAG.23: 10 residues within 4Å: Chain B: N.100, S.102, W.103 Chain F: A.1, V.2, I.4, G.5 Chain G: Y.33, Y.103 Chain H: W.94 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.107, S.109 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.204, T.206, S.244 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.246, T.248, N.249 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.308, W.364 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain C: N.332, S.333, S.357 Ligands: NAG.31, NAG.32 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG.30 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.361 Ligands: NAG.30 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain C: V.104, N.118, S.120, Y.135, D.290 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain C: T.98, Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain C: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.271, Q.408, V.410 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain C: E.57, N.58 Chain D: G.16, S.17 Chain K: Y.107 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain D: N.100, S.102, L.134 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: E.2 Chain D: N.107 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain D: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain E: N.204, T.206, S.244 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain E: N.246, N.249 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain E: N.308, S.362, W.364 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.46: 7 residues within 4Å: Chain E: N.332, S.333, T.341, N.355, S.357 Ligands: NAG.47, NAG.48 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain E: N.355, S.357, R.387 Ligands: NAG.46 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: N.361 Ligands: NAG.46 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain E: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.7 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain E: N.106, N.118, Y.135, D.290 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain C: D.129 Chain E: T.98, Q.100, S.120, N.122 Ligand excluded by PLIP NAG.52: 7 residues within 4Å: Chain E: N.265, N.301, V.302, S.303, S.381, R.412, V.414 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain E: N.271 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain E: E.57, N.58 Chain F: S.17 Ligand excluded by PLIP NAG.55: 9 residues within 4Å: Chain D: A.1, V.2, G.3, I.4 Chain F: N.100, S.102 Chain K: I.101, Y.103 Chain L: W.94 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain F: N.107, L.108, S.109 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain F: E.123, N.126, Y.127 Chain K: G.55, K.57 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morano, N.C. et al., CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO GPZ6-a.01 FAB. To Be Published

Release Date

2024-07-31

Peptides

Envelope glycoprotein gp160: ACE
Envelope glycoprotein gp41: BDF
Antibody GPZ6-a.01 Heavy Chain: GIK
Antibody GPZ6-a.01 Light Chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
N

E
O

B
B

D
H

F
I

G
Q

I
P

K
R

H
T

J
S

L
U

Envelope glycoprotein gp160

Envelope glycoprotein gp41

Antibody GPZ6-a.01 Heavy Chain

Antibody GPZ6-a.01 Light Chain

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