SMTL ID : 9mqg.1

RM017 Fab in complex with Apex-GT6.2 trimer and RM20A3 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

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: 6 residues within 4Å: Chain I: Q.324, T.333, T.334, N.347, S.349 Ligands: NAG.12 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Q.324 NAG-NAG.3: 6 residues within 4Å: Chain I: V.104, T.105, N.106, N.118, Y.135, D.282 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.135 NAG-NAG.5: 5 residues within 4Å: Chain K: T.333, T.334, N.347, S.349 Ligands: NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 8 residues within 4Å: Chain K: P.174, V.216, L.223, N.224, N.338, V.406, S.407 Ligands: NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain K: T.105, N.118, Y.135, L.137, D.282 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:Y.135 NAG-NAG.8: 10 residues within 4Å: Chain A: Y.113, T.115 Chain K: G.98, Q.100, S.120, F.121, N.122, W.150, T.151 Chain M: N.129 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:W.150 NAG-NAG.10: 4 residues within 4Å: Chain M: E.57, N.58 Chain N: G.13, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 9 residues within 4Å: Chain M: E.173, P.174, V.216, L.223, N.224, F.337, V.406, S.407 Ligands: NAG.45 No protein-ligand interaction detected (PLIP)

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.2: 10 residues within 4Å: Chain I: S.171, E.173, P.174, L.223, N.224, N.338, G.340, V.406, S.407 Ligands: NAG.15 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.340

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.4: 12 residues within 4Å: Chain A: S.54, G.55, G.56, N.57, S.71, R.72, D.73, N.74, A.75, Y.112 Chain I: N.122, R.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.54, A:R.72, A:D.73

1 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.9: 8 residues within 4Å: Chain A: Y.110 Chain M: Q.100, S.120, F.121, N.122, R.131, W.150, T.151 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:W.150

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

NAG.12: 4 residues within 4Å: Chain I: Q.324, S.349, N.353 Ligands: NAG-NAG.1 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain I: N.300, W.356 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain I: N.257, T.259, H.291, N.293, R.404 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain I: N.224, S.253, N.408 Ligands: NAG-NAG-BMA-MAN-MAN.2 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain I: N.263, I.284, V.402 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain I: E.57, N.58 Chain J: G.13, S.17 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain I: R.154, N.159 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain I: N.103 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain I: N.196, T.198, I.234, H.313 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain I: N.238, N.241 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain J: N.107, S.109 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain K: Q.324, S.349, N.353 Ligands: NAG-NAG.5, NAG-NAG.5 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain K: S.253, V.406, N.408 Ligands: NAG-NAG.6 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain K: N.103, G.114 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain K: V.144, N.159, T.160 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain K: N.263, I.284, V.402 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain K: N.257, T.259, H.291, N.293, R.404 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain K: Q.255, N.257, N.293, S.295, R.404 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain K: N.238, N.241 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain K: N.196, T.198, S.236, H.313 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain K: E.57, N.58 Chain L: G.13, S.17 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain L: N.107, S.109, E.110 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain L: N.100, S.102 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain L: E.123, N.126 Ligand excluded by PLIP NAG.36: 7 residues within 4Å: Chain M: V.104, T.105, N.106, N.118, Y.135, L.137, D.282 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain M: N.103 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain M: T.333, T.334, N.347, S.349 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain M: S.349, N.353 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain M: N.238, T.240, N.241 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain M: N.196, T.198, S.236 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain M: N.257, T.259, H.291, N.293, R.404 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain M: N.263, I.284, V.402 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain M: Q.255, N.257, N.293, V.406 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain M: N.224, S.253, N.408 Ligands: NAG-NAG.11 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain M: N.300, W.356 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain M: N.316 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain N: N.100, S.102 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain N: K.122, E.123, N.126 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain F: S.107 Chain N: N.107, S.109 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

2025-08-06

Peptides

RM017 Fab heavy chain: A
RM017 Fab light chain: B
RM20A3 Fab light chain: CEH
RM20A3 Fab heavy chain: DFG
Envelope glycoprotein gp120: 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

RM017 Fab heavy chain

RM017 Fab light chain

RM20A3 Fab light chain

RM20A3 Fab heavy chain

Envelope glycoprotein gp120

Transmembrane protein gp41

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