SMTL ID : 8f92.1

HIV Env BG505_MD39_B11 SOSIP boosting trimer in complex with B11_d77.7 mouse 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: 16 residues within 4Å: Chain A: N.265, T.267, D.294, R.296, H.299, N.301, S.381, R.412 Chain E: N.32, S.102, I.103, F.104, G.105, V.106, V.107, Y.113 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.32, E:V.107 NAG-NAG-BMA-MAN-MAN-MAN.4: 16 residues within 4Å: Chain G: N.265, T.267, D.294, R.296, H.299, N.301, S.381, R.412 Chain K: N.32, S.102, I.103, F.104, G.105, V.106, V.107, Y.113 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.32, K:V.107 NAG-NAG-BMA-MAN-MAN-MAN.7: 16 residues within 4Å: Chain M: N.265, T.267, D.294, R.296, H.299, N.301, S.381, R.412 Chain Q: N.32, S.102, I.103, F.104, G.105, V.106, V.107, Y.113 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:N.32, Q:V.107

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: 10 residues within 4Å: Chain A: S.179, E.181, V.224, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.179, A:V.414 NAG-NAG-BMA-MAN.5: 10 residues within 4Å: Chain G: S.179, E.181, V.224, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.35 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.179, G:V.414 NAG-NAG-BMA-MAN.8: 10 residues within 4Å: Chain M: S.179, E.181, V.224, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.50 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:S.179, M:V.414

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: 6 residues within 4Å: Chain A: Q.332, T.341, T.342, N.355, S.357 Ligands: NAG.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.332 NAG-NAG.6: 6 residues within 4Å: Chain G: Q.332, T.341, T.342, N.355, S.357 Ligands: NAG.36 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.332 NAG-NAG.9: 6 residues within 4Å: Chain M: Q.332, T.341, T.342, N.355, S.357 Ligands: NAG.51 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:Q.332

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

NAG.10: 5 residues within 4Å: Chain A: E.57, N.58 Chain D: G.13, G.16, S.17 Ligand excluded by PLIP NAG.11: 6 residues within 4Å: Chain A: Y.104, N.118, Y.135, L.137, G.289, D.290 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: V.144, R.162, N.167, T.168 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: N.204, T.206, S.244, I.247, 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: 3 residues within 4Å: Chain A: N.271, I.292, V.410 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain A: L.235, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN.2 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.3 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: N.107, S.109, E.110 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain D: K.122, E.123, N.126 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain G: E.57, N.58 Chain J: G.13, G.16, S.17 Ligand excluded by PLIP NAG.26: 6 residues within 4Å: Chain G: Y.104, N.118, Y.135, L.137, G.289, D.290 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain G: T.98, Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain G: V.144, R.162, N.167, T.168 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain G: N.204, T.206, S.244, I.247, H.321 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain G: N.246, T.248, N.249 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain G: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain G: N.271, I.292, V.410 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain G: N.308, W.364 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain G: L.235, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN.5 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain G: N.361 Ligands: NAG-NAG.6 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 J: N.107, S.109, E.110 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain J: K.122, E.123, N.126 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain M: E.57, N.58 Chain P: G.13, G.16, S.17 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain M: Y.104, N.118, Y.135, L.137, G.289, D.290 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain M: T.98, Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain M: V.144, R.162, N.167, T.168 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain M: N.204, T.206, S.244, I.247, H.321 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain M: N.246, T.248, N.249 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain M: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain M: N.271, I.292, V.410 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain M: N.308, W.364 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain M: N.324 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain M: L.235, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN.8 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain M: N.361 Ligands: NAG-NAG.9 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain P: N.100, S.102 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain P: N.107, S.109, E.110 Ligand excluded by PLIP NAG.54: 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

Xie, Z. et al., mRNA-LNP HIV-1 trimer boosters elicit precursors to broad neutralizing antibodies. Science (2024)

Release Date

2024-05-15

Peptides

BG505_MD39_B11 gp120: AGM
RM20A3 Fab heavy chain: BHN
RM20A3 Fab light chain: CIO
BG505_MD39_B11 gp41: DJP
B11_d77.7 Fab heavy chain: EKQ
B11_d77.7 Fab kappa light chain: 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

BG505_MD39_B11 gp120

RM20A3 Fab heavy chain

RM20A3 Fab light chain

BG505_MD39_B11 gp41

B11_d77.7 Fab heavy chain

B11_d77.7 Fab kappa light chain

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