SMTL ID : 8t4d.1

MD65 N332-GT5 SOSIP in complex with RM_N332_08 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: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 9 residues within 4Å: Chain A: N.265, T.267, H.299, N.301, I.383, R.412 Chain E: T.28, G.105, F.106 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:T.28 NAG-NAG.2: 6 residues within 4Å: Chain A: Y.104, N.118, Y.135, L.137, G.289, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 9 residues within 4Å: Chain G: N.265, T.267, H.299, N.301, I.383, R.412 Chain K: T.28, G.105, F.106 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:T.28 NAG-NAG.5: 6 residues within 4Å: Chain G: Y.104, N.118, Y.135, L.137, G.289, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 9 residues within 4Å: Chain M: N.265, T.267, H.299, N.301, I.383, R.412 Chain Q: T.28, G.105, F.106 1 PLIP interactions: 1 interactions with chain Q Hydrophobic interactions: Q:T.28 NAG-NAG.8: 6 residues within 4Å: Chain M: Y.104, N.118, Y.135, L.137, G.289, D.290 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.3: 11 residues within 4Å: Chain A: E.181, P.182, L.231, N.232, N.346, C.347, G.348, C.413, V.414, S.415 Ligands: NAG.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.348, A:V.414 NAG-NAG-BMA.6: 11 residues within 4Å: Chain G: E.181, P.182, L.231, N.232, N.346, C.347, G.348, C.413, V.414, S.415 Ligands: NAG.33 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.348, G:V.414 NAG-NAG-BMA.9: 11 residues within 4Å: Chain M: E.181, P.182, L.231, N.232, N.346, C.347, G.348, C.413, V.414, S.415 Ligands: NAG.47 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.10: 3 residues within 4Å: Chain A: N.271, L.292, V.410 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: E.57, N.58 Chain D: S.17 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: T.98, Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: R.162, N.167, T.168 Chain M: R.278 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.204, T.206, S.244, H.321 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.18: 6 residues within 4Å: Chain A: Q.332, T.341, T.342, N.355, S.357, W.387 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.232, S.261, N.416 Ligands: NAG-NAG-BMA.3 Ligand excluded by PLIP NAG.20: 7 residues within 4Å: Chain A: E.238, E.239, V.240, N.259, T.260, K.313, Q.317 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: D.200, N.211 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain G: N.271, L.292, V.410 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain G: E.57, N.58 Chain J: S.17 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain G: T.98, Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: R.278 Chain G: R.162, N.167, T.168 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain G: N.204, T.206, S.244, H.321 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain G: N.246, T.248, N.249 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain G: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain G: N.308, W.364 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain G: Q.332, T.341, T.342, N.355, S.357, W.387 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain G: N.232, S.261, N.416 Ligands: NAG-NAG-BMA.6 Ligand excluded by PLIP NAG.34: 7 residues within 4Å: Chain G: E.238, E.239, V.240, N.259, T.260, K.313, Q.317 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain G: D.200, N.211 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain J: N.100, S.102 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain M: N.271, L.292, V.410 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain M: E.57, N.58 Chain P: S.17 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain M: T.98, Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain G: R.278 Chain M: R.162, N.167, T.168 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain M: N.204, T.206, S.244, H.321 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain M: N.246, T.248, N.249 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain M: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain M: N.308, W.364 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain M: Q.332, T.341, T.342, N.355, S.357, W.387 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain M: N.232, S.261, N.416 Ligands: NAG-NAG-BMA.9 Ligand excluded by PLIP NAG.48: 7 residues within 4Å: Chain M: E.238, E.239, V.240, N.259, T.260, K.313, Q.317 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain M: D.200, N.211 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain M: N.324 Ligand excluded by PLIP NAG.51: 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_08 heavy chain Fv: EKQ
RM_N332_08 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_08 heavy chain Fv

RM_N332_08 light chain Fv

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