SMTL ID : 9bnm.1

Cryo-EM structure of rhesus antibody 44715-a.01 in complex with HIV-1 Env BG505 DS-SOSIP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-3-mer

Ligands

27 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: 6 residues within 4Å: Chain A: N.332, S.333, T.341, N.355 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.1, NAG-NAG.1, NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: E.245, N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: K.320, N.324 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.320 NAG-NAG.7: 4 residues within 4Å: Chain A: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: N.118, Y.135, L.137, D.290, I.291 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.135 Hydrogen bonds: A:Y.135, A:Y.135 NAG-NAG.10: 4 residues within 4Å: Chain A: V.144, R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain A: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: G.358, N.361 Ligands: NAG-NAG.13, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.355, S.357 Ligands: NAG-NAG.12, NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: N.246, T.248, N.249 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.248 NAG-NAG.16: 3 residues within 4Å: Chain B: Q.263, N.265, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain B: V.144, R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain B: E.57, N.58 Chain G: S.16 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain B: T.267, H.299, N.301, S.381, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain B: N.271, T.273, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain B: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain C: N.332, S.333, T.341 Ligands: NAG-NAG.26, NAG-NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain C: G.358, N.361 Ligands: NAG-NAG.26, NAG-NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG.24, NAG-NAG.24, NAG-NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain C: Q.263, N.265 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain C: V.144, R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 5 residues within 4Å: Chain C: T.267, R.296, H.299, N.301, R.412 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.296 NAG-NAG.33: 4 residues within 4Å: Chain C: N.271, I.292, G.409, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 5 residues within 4Å: Chain C: N.204, T.206, S.244, E.245, H.321 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.4: 9 residues within 4Å: Chain A: E.181, P.182, V.224, N.232, N.346, C.347, V.414, S.415 Ligands: NAG.35 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.414 Hydrogen bonds: A:E.181 NAG-NAG-BMA.18: 2 residues within 4Å: Chain B: N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 10 residues within 4Å: Chain C: E.181, P.182, L.231, N.232, N.346, C.347, R.412, V.414, S.415 Ligands: NAG.46 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.414 NAG-NAG-BMA.30: 4 residues within 4Å: Chain C: N.118, K.133, Y.135, D.290 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.135 Hydrogen bonds: C:K.133

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.8: 10 residues within 4Å: Chain A: Q.100, N.122, K.131, K.133 Chain D: E.1, S.25, G.26, F.27, T.28, D.106 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.26, D:T.28

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.14: 11 residues within 4Å: Chain B: E.181, P.182, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.23 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.29: 17 residues within 4Å: Chain C: Q.100, N.122, K.131 Chain D: S.30, H.31, W.33, R.50, D.100, S.102, K.118 Chain E: N.33, K.35, F.37, Y.54, E.55, N.58, D.96 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.30, D:H.31

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

NAG.35: 3 residues within 4Å: Chain A: P.261, N.416 Ligands: NAG-NAG-BMA.4 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain A: C.101, T.102, N.103, K.117 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: E.57, N.58 Chain F: S.16 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: K.304, N.308, W.364 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: P.269, N.271, I.292 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: N.204, T.206, S.244 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.332, S.333 Ligands: NAG-NAG.13 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: G.323, N.324 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: N.103, G.114, K.117 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: N.308, S.362, W.364 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: N.204, T.206, S.244, E.245 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA.27 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: E.245, N.246, T.248, N.249 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: N.103, R.140, S.157 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: E.57, N.58 Chain H: S.16 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: K.304, N.308, W.364 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain G: N.99, S.101 Ligand excluded by PLIP NAG.53: 5 residues within 4Å: Chain H: N.104, R.105, N.106, S.108, E.109 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roark, R.S. et al., Structural and genetic basis of HIV-1 envelope V2 apex recognition by rhesus broadly neutralizing antibodies. J.Exp.Med. (2025)

Release Date

2025-05-07

Peptides

Envelope glycoprotein Gp120: ABC
47715-a.01 heavy chain: D
44715-a.01 light chain: E
Envelope glycoprotein Gp41: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

F
X

G
Y

H
Z

Envelope glycoprotein Gp120

47715-a.01 heavy chain

44715-a.01 light chain

Envelope glycoprotein Gp41

Related Entries With Identical Sequence