SMTL ID : 9dmb.1

Rhesus RHA10.01 Fab in complex with HIV-1 Env BG505 DS-SOSIP trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 5 residues within 4Å: Chain J: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain J: H.299, N.301 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain J: T.102, N.103, R.113, Y.161 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:Y.161 NAG-NAG.12: 1 residues within 4Å: Chain J: N.430 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain K: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain K: H.299, N.301 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain K: T.102, N.103, R.113, Y.161 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Y.161 NAG-NAG.24: 1 residues within 4Å: Chain K: N.430 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain L: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain L: H.299, N.301 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain L: T.102, N.103, R.113, Y.161 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Y.161 NAG-NAG.36: 1 residues within 4Å: Chain L: N.430 No protein-ligand interaction detected (PLIP)

9 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.2: 8 residues within 4Å: Chain J: E.181, P.182, L.231, N.232, N.346, V.414, S.415 Ligands: NAG.48 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.5: 6 residues within 4Å: Chain J: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.7: 11 residues within 4Å: Chain G: I.32, S.33 Chain J: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.5, NAG-NAG-BMA-MAN-MAN.5, NAG-NAG-BMA-MAN-MAN.5, NAG-NAG-BMA-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.14: 8 residues within 4Å: Chain K: E.181, P.182, L.231, N.232, N.346, V.414, S.415 Ligands: NAG.55 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 6 residues within 4Å: Chain K: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.19, NAG-NAG-BMA-MAN-MAN.19, NAG-NAG-BMA-MAN-MAN.19, NAG-NAG-BMA-MAN-MAN.19 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.19: 11 residues within 4Å: Chain D: I.32, S.33 Chain K: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.17, NAG-NAG-BMA-MAN-MAN.17, NAG-NAG-BMA-MAN-MAN.17, NAG-NAG-BMA-MAN-MAN.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.26: 8 residues within 4Å: Chain L: E.181, P.182, L.231, N.232, N.346, V.414, S.415 Ligands: NAG.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.29: 6 residues within 4Å: Chain L: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.31, NAG-NAG-BMA-MAN-MAN.31, NAG-NAG-BMA-MAN-MAN.31, NAG-NAG-BMA-MAN-MAN.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.31: 11 residues within 4Å: Chain A: I.32, S.33 Chain L: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.29, NAG-NAG-BMA-MAN-MAN.29, NAG-NAG-BMA-MAN-MAN.29, NAG-NAG-BMA-MAN-MAN.29 No protein-ligand interaction detected (PLIP)

15 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: 1 residues within 4Å: Chain J: N.361 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain J: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 3 residues within 4Å: Chain J: N.167, T.168 Chain L: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 5 residues within 4Å: Chain J: Q.263, I.264, N.265, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 3 residues within 4Å: Chain J: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 1 residues within 4Å: Chain K: N.361 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 3 residues within 4Å: Chain K: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain J: R.278 Chain K: N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 5 residues within 4Å: Chain K: Q.263, I.264, N.265, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 3 residues within 4Å: Chain K: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 1 residues within 4Å: Chain L: N.361 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 3 residues within 4Å: Chain L: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.32: 3 residues within 4Å: Chain K: R.278 Chain L: N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.34: 5 residues within 4Å: Chain L: Q.263, I.264, N.265, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 3 residues within 4Å: Chain L: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP)

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

NAG.37: 2 residues within 4Å: Chain C: N.100, S.102 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: K.122, S.125, N.126 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain F: K.122, S.125, N.126 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain I: N.100, S.102 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain I: K.122, S.125, N.126 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain I: S.17 Chain J: E.57, N.58 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain J: N.271, I.292, V.410 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain J: N.308, S.362, W.364 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain J: K.320, N.324 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain J: N.106, N.107, I.291, G.293 Ligand excluded by PLIP NAG.48: 6 residues within 4Å: Chain J: P.261, Q.263, V.414, S.415, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.2 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain J: Q.100, N.122 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain F: S.17 Chain K: E.57, N.58 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain K: N.271, I.292, V.410 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain K: N.308, S.362, W.364 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain K: K.320, N.324 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain K: N.106, N.107, I.291, G.293 Ligand excluded by PLIP NAG.55: 6 residues within 4Å: Chain K: P.261, Q.263, V.414, S.415, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.14 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain K: Q.100, N.122 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain C: S.17 Chain L: E.57, N.58 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain L: N.271, I.292, V.410 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain L: N.308, S.362, W.364 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain L: K.320, N.324 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain L: N.106, N.107, I.291, G.293 Ligand excluded by PLIP NAG.62: 6 residues within 4Å: Chain L: P.261, Q.263, V.414, S.415, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.26 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain L: Q.100, N.122 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, J. et al., Transient glycan-shield reduction induces CD4-binding site broadly neutralizing antibodies in SHIV-infected macaques neutralizing antibodies in SHIV-infected rhesus macaques. Cell Rep (2025)

Release Date

2025-06-18

Peptides

RHA10.01 Light chain: ADG
RHA10.01 Heavy chain: BEH
BG505 DS-SOSIP glycoprotein gp41: CFI
Envelope glycoprotein gp120: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
D

B
C

E
G

H
H

C
E

F
I

I
J

J
L

K
F

L
K

RHA10.01 Light chain

RHA10.01 Heavy chain

BG505 DS-SOSIP glycoprotein gp41

Envelope glycoprotein gp120

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