SMTL ID : 9msy.1

G002-480-0546 Fab in complex with V703-0537_T278M_L14 SOSIP and BG18 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

hetero-3-3-3-3-3-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: 7 residues within 4Å: Chain A: N.215, T.217, F.218, P.223, N.225 Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: E.253, D.254, N.274, E.275, R.328, E.331 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: S.276, S.418, S.419, N.420 Ligands: NAG-NAG-BMA-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.286, I.307 Ligands: NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 7 residues within 4Å: Chain F: N.215, T.217, F.218, P.223, N.225 Ligands: NAG-NAG-BMA.9, NAG-NAG-BMA.9 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain F: E.253, D.254, N.274, E.275, R.328, E.331 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain F: S.276, S.418, S.419, N.420 Ligands: NAG-NAG-BMA-MAN-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain F: N.286, I.307 Ligands: NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 7 residues within 4Å: Chain K: N.215, T.217, F.218, P.223, N.225 Ligands: NAG-NAG-BMA.16, NAG-NAG-BMA.16 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain K: E.253, D.254, N.274, E.275, R.328, E.331 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain K: S.276, S.418, S.419, N.420 Ligands: NAG-NAG-BMA-MAN-MAN.19 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain K: N.286, I.307 Ligands: NAG.44 No protein-ligand interaction detected (PLIP)

3 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.2: 6 residues within 4Å: Chain A: N.219, T.221, I.257, S.259 Ligands: NAG-NAG.1, NAG-NAG.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 6 residues within 4Å: Chain F: N.219, T.221, I.257, S.259 Ligands: NAG-NAG.8, NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 6 residues within 4Å: Chain K: N.219, T.221, I.257, S.259 Ligands: NAG-NAG.15, NAG-NAG.15 No protein-ligand interaction detected (PLIP)

3 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.5: 11 residues within 4Å: Chain A: K.192, S.194, D.196, K.237, L.246, N.247, N.360, R.362, S.418, S.419 Ligands: NAG-NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.418 NAG-NAG-BMA-MAN-MAN.12: 11 residues within 4Å: Chain F: K.192, S.194, D.196, K.237, L.246, N.247, N.360, R.362, S.418, S.419 Ligands: NAG-NAG.11 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.418 NAG-NAG-BMA-MAN-MAN.19: 11 residues within 4Å: Chain K: K.192, S.194, D.196, K.237, L.246, N.247, N.360, R.362, S.418, S.419 Ligands: NAG-NAG.18 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.418

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.6: 14 residues within 4Å: Chain A: E.280, T.282, D.309, H.314, N.316 Chain B: R.29, I.103, G.105, V.106, V.107, F.113 Chain C: S.50, S.51 Ligands: NAG.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.107, B:R.29 NAG-NAG-BMA-MAN-MAN-MAN.13: 14 residues within 4Å: Chain F: E.280, T.282, D.309, H.314, N.316 Chain G: R.29, I.103, G.105, V.106, V.107, F.113 Chain H: S.50, S.51 Ligands: NAG.36 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:V.107, G:R.29 NAG-NAG-BMA-MAN-MAN-MAN.20: 14 residues within 4Å: Chain K: E.280, T.282, D.309, H.314, N.316 Chain L: R.29, I.103, G.105, V.106, V.107, F.113 Chain M: S.50, S.51 Ligands: NAG.44 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:V.107, L:R.29

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

NAG.22: 3 residues within 4Å: Chain A: N.214, N.225, N.226 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: E.60, N.61, S.509 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.142, K.153 Chain F: D.149 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.103 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain A: V.164, I.166, N.182, T.183 Chain E: S.75 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: N.592, T.594, W.595, T.622 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain A: P.284, R.311, N.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6, NAG-NAG.7 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.26 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain F: N.214, N.225, N.226 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain F: E.60, N.61, S.509 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain F: N.142, K.153 Chain K: D.149 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain F: N.103 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain F: V.164, I.166, N.182, T.183 Chain J: S.75 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain F: N.592, T.594, W.595, T.622 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain F: P.284, R.311, N.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.13, NAG-NAG.14 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain G: N.26 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain K: N.214, N.225, N.226 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain K: E.60, N.61, S.509 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: D.149 Chain K: N.142, K.153 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain K: N.103 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain K: V.164, I.166, N.182, T.183 Chain O: S.75 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain K: N.592, T.594, W.595, T.622 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain K: P.284, R.311, N.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.20, NAG-NAG.21 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain L: N.26 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Willis, J.R. et al., Vaccination with mRNA-encoded nanoparticles drives early maturation of HIV bnAb precursors in humans. Science (2025)

Release Date

2025-05-28

Peptides

V703-0537_T278M_L14 SOSIP: AFK
BG18 Fab heavy chain: BGL
BG18 Fab light chain: CHM
G002-480-0546 Fab light chain: DIN
G002-480-0546 Fab heavy chain: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
B

K
C

B
G

G
J

L
O

C
I

H
M

M
Q

D
L

I
N

N
R

E
H

J
K

O
P

V703-0537_T278M_L14 SOSIP

BG18 Fab heavy chain

BG18 Fab light chain

G002-480-0546 Fab light chain

G002-480-0546 Fab heavy chain

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