SMTL ID : 8t4b.1

MD65 N332-GT5 SOSIP in complex with RM_N332_32 Fab and RM20A3

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: 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.1: 11 residues within 4Å: Chain A: N.265, T.267, R.296, H.299, N.301, I.383 Chain E: V.103, G.105, V.106, V.107 Ligands: NAG.15 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:R.296, E:V.107 Hydrophobic interactions: E:V.107 NAG-NAG-BMA-MAN-MAN.3: 11 residues within 4Å: Chain G: N.265, T.267, R.296, H.299, N.301, I.383 Chain K: V.103, G.105, V.106, V.107 Ligands: NAG.29 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain G Hydrophobic interactions: K:V.107 Hydrogen bonds: K:V.107, G:R.296 NAG-NAG-BMA-MAN-MAN.5: 11 residues within 4Å: Chain M: N.265, T.267, R.296, H.299, N.301, I.383 Chain Q: V.103, G.105, V.106, V.107 Ligands: NAG.43 3 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain M Hydrophobic interactions: Q:V.107 Hydrogen bonds: Q:V.107, M:R.296

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.2: 9 residues within 4Å: Chain A: E.181, P.182, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.348, A:V.414 NAG-NAG-BMA-MAN.4: 9 residues within 4Å: Chain G: E.181, P.182, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.32 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.348, G:V.414 NAG-NAG-BMA-MAN.6: 9 residues within 4Å: Chain M: E.181, P.182, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.46 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:G.348, M:V.414

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

NAG.7: 6 residues within 4Å: Chain A: E.238, E.239, N.259, T.260, K.313, Q.317 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.271, L.292, V.410 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: E.57, N.58 Chain D: G.16, S.17 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.118, L.137, G.289, D.290 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: R.162, N.167 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.204, S.244, I.247, H.321 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.15: 7 residues within 4Å: Chain A: Q.263, N.265, N.301, I.302, S.303, R.412 Ligands: NAG-NAG-BMA-MAN-MAN.1 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.308 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: T.341, T.342, N.355, S.357 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN.2 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: D.200, K.201, N.211 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain G: E.238, E.239, N.259, T.260, K.313, Q.317 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain G: N.271, L.292, V.410 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain G: E.57, N.58 Chain J: G.16, S.17 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain G: N.118, L.137, G.289, D.290 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain G: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain G: R.162, N.167 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain G: N.204, S.244, I.247, H.321 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain G: N.246, T.248, N.249 Ligand excluded by PLIP NAG.29: 7 residues within 4Å: Chain G: Q.263, N.265, N.301, I.302, S.303, R.412 Ligands: NAG-NAG-BMA-MAN-MAN.3 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain G: N.308 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain G: T.341, T.342, N.355, S.357 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain G: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN.4 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain G: D.200, K.201, N.211 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain J: N.100, S.102 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain M: E.238, E.239, N.259, T.260, K.313, Q.317 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain M: N.271, L.292, V.410 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain M: E.57, N.58 Chain P: G.16, S.17 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain M: N.118, L.137, G.289, D.290 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain M: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain M: R.162, N.167 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain M: N.204, S.244, I.247, H.321 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain M: N.246, T.248, N.249 Ligand excluded by PLIP NAG.43: 7 residues within 4Å: Chain M: Q.263, N.265, N.301, I.302, S.303, R.412 Ligands: NAG-NAG-BMA-MAN-MAN.5 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain M: N.308 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain M: T.341, T.342, N.355, S.357 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain M: N.232, S.261, N.416 Ligands: NAG-NAG-BMA-MAN.6 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain M: D.200, K.201, N.211 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain P: N.100, S.102 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_32 heavy chain Fv: EKQ
RM_N332_32 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_32 heavy chain Fv

RM_N332_32 light chain Fv

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