SMTL ID : 9b8b.1

RM038 Fab in complex with Apex-GT 6.2 trimer and RM20A3 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 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: 4 residues within 4Å: Chain I: N.288, T.290, N.324, T.406 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain I: N.378, S.380 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 9 residues within 4Å: Chain A: R.102, G.103, F.114 Chain K: Q.131, S.151, F.152, N.153, W.181, T.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.102 NAG-NAG.6: 4 residues within 4Å: Chain K: N.255, S.284, N.439 Ligands: NAG-NAG-BMA.5 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain K: Q.355, N.378, S.380, P.408 Ligands: NAG.40 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Q.355 NAG-NAG.8: 7 residues within 4Å: Chain M: V.135, T.136, N.137, N.149, S.151, Y.166, D.313 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:Y.166 NAG-NAG.9: 6 residues within 4Å: Chain M: Q.131, S.151, F.152, N.153, K.164, W.181 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain M: T.364, T.365, N.378, S.380 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: 9 residues within 4Å: Chain I: E.204, P.205, V.247, L.254, N.255, N.369, V.437, S.438 Ligands: NAG.20 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:V.437 NAG-NAG-BMA.5: 11 residues within 4Å: Chain K: E.204, P.205, V.247, L.254, N.255, N.369, G.371, C.436, V.437, S.438 Ligands: NAG-NAG.6 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:G.371, K:V.437 NAG-NAG-BMA.10: 11 residues within 4Å: Chain M: E.204, P.205, V.247, L.254, N.255, N.369, G.371, C.436, V.437, S.438 Ligands: NAG.56 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:G.371, M:V.437

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

NAG.12: 3 residues within 4Å: Chain I: E.88, N.89 Chain J: S.17 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain I: N.134 Ligand excluded by PLIP NAG.14: 7 residues within 4Å: Chain I: V.135, T.136, N.137, N.149, Y.166, L.168, D.313 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: G.56, D.58 Chain I: N.153, R.162 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain I: R.185, N.190, T.191 Chain K: R.301 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain I: N.227, T.229, S.267, I.270, H.344 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain I: N.269, T.271 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain I: Q.286, N.288, S.326, V.437 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain I: N.255, N.439 Ligands: NAG-NAG-BMA.2 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain I: E.260, E.261, E.262, N.282, T.283, K.336 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain I: K.222, N.234 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain I: N.294, I.315, V.433 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain J: N.100 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain J: N.107, S.109, E.110 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain J: K.122, N.126 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain K: E.88, N.89 Chain L: S.17 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain K: N.134, K.148 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain K: N.138 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain K: V.135, T.136, N.149, Y.166, L.168, D.313 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain K: R.185, N.190, T.191 Chain M: R.301 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain K: N.227, T.229, S.267 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain K: N.234 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain K: N.269, T.271, N.272 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain K: E.260, E.261, N.282, T.283, K.336 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain K: Q.286, N.288, N.324, S.326 Ligands: NAG.38 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain K: N.294, I.315, V.433 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain K: T.290, H.322, N.324, R.435 Ligands: NAG.36 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain K: N.347 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain K: S.380, N.384 Ligands: NAG-NAG.7 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain L: N.100, S.102, I.130 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain L: N.105, N.107, S.109, E.110 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain L: N.126 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain L: T.18, N.114 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain M: E.88, N.89 Chain N: G.13, S.17 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain M: R.185, N.190, T.191 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain M: N.227, T.229, S.267 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain M: N.234 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain M: N.269, T.271, N.272 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain M: E.261, E.262, N.282, T.283, K.336 Ligand excluded by PLIP NAG.51: 7 residues within 4Å: Chain M: Q.286, N.288, N.324, S.326, R.435, V.437 Ligands: NAG.52 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain M: T.290, H.322, N.324, R.435 Ligands: NAG.51 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain M: N.294, I.315, V.433 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain M: N.331, E.332, W.387 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain M: S.380, N.384 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain M: S.284, N.439 Ligands: NAG-NAG-BMA.10 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain N: N.100, S.102 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain N: N.107, S.109, E.110 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain N: N.114, M.115, Q.119 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain N: N.126 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

RM038 fragment antigen binding heavy chain: A
RM038 fragment antigen binding light chain: B
RM20A3 fragment antigen binding light chain: CEH
RM20A3 fragment antigen binding heavy chain: DFG
Envelope glycoprotein gp160: IKM
Transmembrane protein gp41: JLN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
G

E
J

H
N

D
I

F
K

G
M

I
A

K
C

M
D

J
B

L
E

N
F

RM038 fragment antigen binding heavy chain

RM038 fragment antigen binding light chain

RM20A3 fragment antigen binding light chain

RM20A3 fragment antigen binding heavy chain

Envelope glycoprotein gp160

Transmembrane protein gp41

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