SMTL ID : 8t4a.1

MD65 N332-GT5 SOSIP in complex with RM_N332_36 Fab and RM20A3 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 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.1: 13 residues within 4Å: Chain A: N.265, T.267, H.294, H.299, N.301, I.383, R.412 Chain E: S.103, V.104, W.105, G.106, V.107, L.108 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.103, E:L.108 Hydrophobic interactions: E:L.108 NAG-NAG-BMA-MAN.2: 9 residues within 4Å: Chain A: E.181, P.182, V.224, L.231, N.232, G.348, V.414, S.415 Ligands: NAG.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.181, A:G.348 NAG-NAG-BMA-MAN.4: 13 residues within 4Å: Chain G: N.265, T.267, H.294, H.299, N.301, I.383, R.412 Chain K: S.103, V.104, W.105, G.106, V.107, L.108 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:S.103, K:L.108 Hydrophobic interactions: K:L.108 NAG-NAG-BMA-MAN.5: 9 residues within 4Å: Chain G: E.181, P.182, V.224, L.231, N.232, G.348, V.414, S.415 Ligands: NAG.36 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.181, G:G.348 NAG-NAG-BMA-MAN.7: 13 residues within 4Å: Chain M: N.265, T.267, H.294, H.299, N.301, I.383, R.412 Chain Q: S.103, V.104, W.105, G.106, V.107, L.108 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:S.103, Q:L.108 Hydrophobic interactions: Q:L.108 NAG-NAG-BMA-MAN.8: 9 residues within 4Å: Chain M: E.181, P.182, V.224, L.231, N.232, G.348, V.414, S.415 Ligands: NAG.53 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:E.181, M:G.348

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.3: 5 residues within 4Å: Chain A: Q.332, T.342, N.355, S.357 Ligands: NAG.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.332 NAG-NAG.6: 5 residues within 4Å: Chain G: Q.332, T.342, N.355, S.357 Ligands: NAG.40 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.332 NAG-NAG.9: 5 residues within 4Å: Chain M: Q.332, T.342, N.355, S.357 Ligands: NAG.57 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:Q.332

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

NAG.10: 3 residues within 4Å: Chain A: N.271, L.292, V.410 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: E.57, N.58 Chain D: G.16, S.17 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.118, L.137 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: V.144, R.162, N.167 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.204, T.206, S.244, I.247, H.321 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.308, E.309, W.364 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN.2 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: E.238, N.259, T.260, K.313 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: K.199, N.211 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: R.319, K.320, G.323, N.324 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG-NAG.3, NAG-NAG.3 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain D: N.107, E.110 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain D: K.122, E.123, N.126 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain G: N.271, L.292, V.410 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain G: E.57, N.58 Chain J: G.16, S.17 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain G: N.118, L.137 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain G: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain G: V.144, R.162, N.167 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain G: N.204, T.206, S.244, I.247, H.321 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain G: N.246, T.248, N.249 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain G: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain G: N.308, E.309, W.364 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain G: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN.5 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain G: E.238, N.259, T.260, K.313 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain G: K.199, N.211 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain G: R.319, K.320, G.323, N.324 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain G: S.357, N.361 Ligands: NAG-NAG.6, NAG-NAG.6 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain J: N.100, S.102 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain J: N.107, E.110 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain J: K.122, E.123, N.126 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain M: N.271, L.292, V.410 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain M: E.57, N.58 Chain P: G.16, S.17 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain M: N.118, L.137 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain M: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain M: V.144, R.162, N.167 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain M: N.204, T.206, S.244, I.247, H.321 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain M: N.246, T.248, N.249 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain M: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain M: N.308, E.309, W.364 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain M: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN.8 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain M: E.238, N.259, T.260, K.313 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain M: K.199, N.211 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain M: R.319, K.320, G.323, N.324 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain M: S.357, N.361 Ligands: NAG-NAG.9, NAG-NAG.9 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain P: N.100, S.102 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain P: N.107, E.110 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain P: K.122, E.123, N.126 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
RM20A3 heavy chain Fv: BHN
RM20A3 light chain Fv: CIO
MD65 N332-GT5 SOSIP gp41: DJP
RM_N332_36 heavy chain Fv: EKQ
RM_N332_36 light chain Fv: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
E

M
F

B
C

H
J

N
K

C
D

I
M

O
N

D
B

J
G

P
I

E
H

K
O

Q
P

F
L

L
Q

R
R

MD65 N332-GT5 SOSIP gp120

RM20A3 heavy chain Fv

RM20A3 light chain Fv

MD65 N332-GT5 SOSIP gp41

RM_N332_36 heavy chain Fv

RM_N332_36 light chain Fv

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