SMTL ID : 9b8c.1

RM018 Fab in complex with Apex GT 6.2 trimer and RM20A3 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-1-3-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1: 21 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122, K.133 Chain H: V.55, G.56, I.57, T.58, Y.60, Q.65, G.66, R.67, V.68, T.69, I.70, T.71, A.72, D.73, S.84, Y.112 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain A Hydrogen bonds: H:T.58, H:T.58, H:A.72, H:G.56, H:T.58, H:T.58, A:Q.100

7 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 8 residues within 4Å: Chain A: E.173, P.174, V.216, N.224, F.337, N.338, V.406, S.407 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.406 NAG-NAG.3: 2 residues within 4Å: Chain A: N.159, T.160 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain C: G.98, Q.100, S.120, N.122, W.150, T.151 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain C: V.104, T.105, N.118, S.120, Y.135, D.282 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.135 NAG-NAG.7: 6 residues within 4Å: Chain D: G.98, Q.100, S.120, N.122, W.150, T.151 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.150 NAG-NAG.8: 5 residues within 4Å: Chain A: R.270 Chain D: V.144, R.154, N.159, T.160 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.144 NAG-NAG.9: 5 residues within 4Å: Chain D: V.104, T.105, N.118, Y.135, D.282 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.135

2 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.6: 7 residues within 4Å: Chain C: E.173, P.174, L.223, N.224, V.406, S.407 Ligands: NAG.31 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.173, C:V.406 NAG-NAG-BMA.10: 9 residues within 4Å: Chain D: V.216, L.223, N.224, N.338, C.339, G.340, V.406, S.407 Ligands: NAG.49 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.406

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

NAG.11: 5 residues within 4Å: Chain A: T.105, N.118, Y.135, L.137, D.282 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: T.333, T.334, N.347, S.349 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: S.349, N.353 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.103 Chain H: Q.65 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: E.57, N.58 Chain B: S.17 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: H.55, K.191, N.203 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.196, T.198, S.236, H.313 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.263, I.284, G.401, V.402 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: Q.255, N.257 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain A: T.259, H.291, N.293, T.375, R.404 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: S.253, N.408 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain A: E.230, E.231, N.251, T.252, K.305 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.238, T.240, N.241 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: R.311, G.315, N.316 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: K.122, E.123, N.126 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.107, S.109 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: N.263, I.284, G.401, V.402 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain C: N.257, H.291, N.293, R.404 Ligands: NAG.30 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain C: Q.255, N.257, R.404, V.406 Ligands: NAG.29 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: S.253, N.408 Ligands: NAG-NAG-BMA.6 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: T.333, T.334, N.347, S.349 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: V.144, N.159, T.160 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.196, T.198, S.236 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.251, T.252, K.305 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: E.57, N.58 Chain E: S.17 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: K.191, N.203 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.103, R.113, K.117 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.238, T.240, N.241 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain D: N.263, I.284, V.402 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain D: T.333, T.334, N.347, S.349 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain D: T.259, H.291, N.293, T.375, R.404 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain D: Q.255, N.257, S.295, R.404 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain D: N.238, T.240, N.241 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain D: N.103, G.114 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain D: E.57, N.58 Chain F: S.17 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain D: N.196, T.198, S.236, H.313 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain D: E.229, E.231, N.251, T.252, K.305 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain D: S.253, N.408 Ligands: NAG-NAG-BMA.10 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain D: K.191, N.203 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain D: N.316 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain D: N.353 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain E: N.107, S.109, E.110 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain E: E.123, S.125, N.126, Y.127 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain E: N.100, S.102 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain F: N.107, S.109 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain F: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, K.M. et al., HIV broadly neutralizing antibody precursors to the Apex epitope induced in nonhuman primates. Sci Immunol (2025)

Release Date

2025-07-30

Peptides

Envelope glycoprotein gp120: ACD
Transmembrane protein gp41: BEF
RM20A3 fragment antigen binding light chain: GJN
RM018 fragment antigen binding heavy chain: H
RM20A3 fragment antigen binding heavy chain: IKM
RM018 fragment antigen binding light chain: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

B
B

E
E

F
F

G
G

J
J

N
N

H
H

I
I

K
K

M
M

L
L

Envelope glycoprotein gp120

Transmembrane protein gp41

RM20A3 fragment antigen binding light chain

RM018 fragment antigen binding heavy chain

RM20A3 fragment antigen binding heavy chain

RM018 fragment antigen binding light chain

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