SMTL ID : 8t49.1

MD65 N332-GT5 SOSIP in complex with RM_N332_03 Fab and RM20A3 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 9 residues within 4Å: Chain A: N.265, T.267, H.299, N.301, I.383 Chain B: I.104, G.106, V.107, V.108 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.108 NAG-NAG-BMA-MAN-MAN-MAN.5: 9 residues within 4Å: Chain G: N.265, T.267, H.299, N.301, I.383 Chain H: I.104, G.106, V.107, V.108 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:V.108 NAG-NAG-BMA-MAN-MAN-MAN.9: 9 residues within 4Å: Chain M: N.265, T.267, H.299, N.301, I.383 Chain N: I.104, G.106, V.107, V.108 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:V.108

3 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: 3 residues within 4Å: Chain A: N.118, Y.135, L.137 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain G: N.118, Y.135, L.137 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain M: N.118, Y.135, L.137 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: 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.3: 8 residues within 4Å: Chain A: S.179, E.181, P.182, L.231, N.232, V.414, S.415 Ligands: NAG.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.179, A:S.179, A:V.414 NAG-NAG-BMA-MAN.7: 8 residues within 4Å: Chain G: S.179, E.181, P.182, L.231, N.232, V.414, S.415 Ligands: NAG.39 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.179, G:S.179, G:V.414 NAG-NAG-BMA-MAN.11: 8 residues within 4Å: Chain M: S.179, E.181, P.182, L.231, N.232, V.414, S.415 Ligands: NAG.56 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:S.179, M:S.179, M:V.414

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.4: 4 residues within 4Å: Chain B: R.39, K.44, E.47, N.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain H: R.39, K.44, E.47, N.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 4 residues within 4Å: Chain N: R.39, K.44, E.47, N.62 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: N.271, L.292, V.410 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: E.57, N.58 Chain F: S.17 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: V.144, R.162, N.167 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.204, T.206, S.244, H.321 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.21: 7 residues within 4Å: Chain A: Q.332, T.341, T.342, N.355, S.357, W.387 Ligands: NAG.26 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN.3 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: E.238, N.259, T.260, K.313 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: D.200, K.201, N.211 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: Q.332, N.361 Ligands: NAG.21 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain F: N.107, E.110 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain F: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain G: N.271, L.292, V.410 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain G: E.57, N.58 Chain L: S.17 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain G: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain G: V.144, R.162, N.167 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain G: N.204, T.206, S.244, H.321 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain G: N.246, T.248, N.249 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain G: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain G: N.308, W.364 Ligand excluded by PLIP NAG.38: 7 residues within 4Å: Chain G: Q.332, T.341, T.342, N.355, S.357, W.387 Ligands: NAG.43 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain G: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN.7 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain G: E.238, N.259, T.260, K.313 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain G: D.200, K.201, N.211 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain G: Q.332, N.361 Ligands: NAG.38 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain L: N.100, S.102 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain L: N.107, E.110 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain L: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain M: N.271, L.292, V.410 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain M: E.57, N.58 Chain R: S.17 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain M: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain M: V.144, R.162, N.167 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain M: N.204, T.206, S.244, H.321 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain M: N.246, T.248, N.249 Ligand excluded by PLIP NAG.53: 5 residues within 4Å: Chain M: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain M: N.308, W.364 Ligand excluded by PLIP NAG.55: 7 residues within 4Å: Chain M: Q.332, T.341, T.342, N.355, S.357, W.387 Ligands: NAG.60 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain M: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN.11 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain M: E.238, N.259, T.260, K.313 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain M: D.200, K.201, N.211 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain M: N.324 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain M: Q.332, N.361 Ligands: NAG.55 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain R: N.100, S.102 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain R: N.107, E.110 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain R: E.123, N.126, Y.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steichen, J.M. et al., Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates. Science (2024)

Release Date

2024-05-08

Peptides

MD65 N332-GT5 SOSIP gp120: AGM
RM_N332_03 heavy chain Fv: BHN
RM_N332_03 light chain Fv: CIO
RM20A3 heavy chain Fv: DJP
RM20A3 light chain Fv: EKQ
MD65 N332-GT5 SOSIP gp41: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
E

M
F

B
H

H
O

N
P

C
L

I
Q

O
R

D
C

J
J

P
K

E
D

K
M

Q
N

F
B

L
G

R
I

MD65 N332-GT5 SOSIP gp120

RM_N332_03 heavy chain Fv

RM_N332_03 light chain Fv

RM20A3 heavy chain Fv

RM20A3 light chain Fv

MD65 N332-GT5 SOSIP gp41

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