SMTL ID : 6nf5.1

BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP1 fragmentantigen binding and base-binding RM20A3 fragment antigen binding

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

15 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: 6 residues within 4Å: Chain A: Y.104, N.118, Y.135, L.137, G.289, D.290 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.135 NAG-NAG.3: 5 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: Q.332, T.341, T.342, N.355, S.357 Ligands: NAG.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.332 NAG-NAG.6: 3 residues within 4Å: Chain A: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain G: Y.104, N.118, Y.135, L.137, G.289, D.290 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.135 NAG-NAG.10: 5 residues within 4Å: Chain G: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain G: Q.332, T.341, T.342, N.355, S.357 Ligands: NAG.37 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.332 NAG-NAG.13: 3 residues within 4Å: Chain G: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain H: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain M: Y.104, N.118, Y.135, L.137, G.289, D.290 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:Y.135 NAG-NAG.17: 5 residues within 4Å: Chain M: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain M: Q.332, T.341, T.342, N.355, S.357 Ligands: NAG.48 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:Q.332 NAG-NAG.20: 3 residues within 4Å: Chain M: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain N: N.100, S.102 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.2: 11 residues within 4Å: Chain A: S.179, P.182, L.231, N.232, N.346, G.348, I.407, Q.408, V.414, S.415 Ligands: NAG.27 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.414 Hydrogen bonds: A:G.348, A:V.414, A:Q.408, A:Q.408 NAG-NAG-BMA-MAN-MAN.9: 11 residues within 4Å: Chain G: S.179, P.182, L.231, N.232, N.346, G.348, I.407, Q.408, V.414, S.415 Ligands: NAG.38 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:V.414 Hydrogen bonds: G:G.348, G:V.414, G:Q.408, G:Q.408 NAG-NAG-BMA-MAN-MAN.16: 11 residues within 4Å: Chain M: S.179, P.182, L.231, N.232, N.346, G.348, I.407, Q.408, V.414, S.415 Ligands: NAG.49 2 PLIP interactions: 2 interactions with chain M Hydrophobic interactions: M:V.414 Hydrogen bonds: M:G.348, M:V.414, M:Q.408, M:Q.408

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.4: 12 residues within 4Å: Chain A: N.265, T.267, H.299, N.301, S.381, I.383, R.412 Chain C: I.104, F.105, G.106, V.107, V.108 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.108 Hydrogen bonds: C:V.108 NAG-NAG-BMA-MAN-MAN-MAN.11: 12 residues within 4Å: Chain G: N.265, T.267, H.299, N.301, S.381, I.383, R.412 Chain I: I.104, F.105, G.106, V.107, V.108 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:V.108 Hydrogen bonds: I:V.108 NAG-NAG-BMA-MAN-MAN-MAN.18: 12 residues within 4Å: Chain M: N.265, T.267, H.299, N.301, S.381, I.383, R.412 Chain O: I.104, F.105, G.106, V.107, V.108 2 PLIP interactions: 2 interactions with chain O Hydrophobic interactions: O:V.108 Hydrogen bonds: O:V.108

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

NAG.22: 4 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain A: V.144, R.162, L.163, I.164, N.167 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.271, L.292, V.410 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: Q.332, S.357, N.361 Ligands: NAG-NAG.5 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.2 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, S.17 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: N.204, T.206, S.244, I.247 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.107, S.109 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain G: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain G: V.144, R.162, L.163, I.164, N.167 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain G: N.271, L.292, V.410 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain G: N.308, W.364 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain G: Q.332, S.357, N.361 Ligands: NAG-NAG.12 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain G: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.9 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain G: E.57, N.58 Chain H: G.16, S.17 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain G: N.204, T.206, S.244, I.247 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain H: N.107, S.109 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain H: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain M: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain M: V.144, R.162, L.163, I.164, N.167 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain M: N.271, L.292, V.410 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain M: N.308, W.364 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain M: Q.332, S.357, N.361 Ligands: NAG-NAG.19 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain M: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.16 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain M: E.57, N.58 Chain N: G.16, S.17 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain M: N.204, T.206, S.244, I.247 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain M: N.324 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain N: N.107, S.109 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain N: K.122, E.123, S.125, N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steichen, J.M. et al., A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses. Science (2019)

Release Date

2019-11-06

Peptides

HIV-1 Env BG505 MD64 N332-GT5 SOSIP gp120: AGM
HIV-1 Env BG505 MD64 N332-GT5 SOSIP gp41: BHN
BG18-like precursor HMP1 fragment antigen binding heavy chain: CIO
BG18-like precursor HMP1 fragment antigen binding light chain: DJP
base-binding RM20A3 fragment antigen binding heavy chain: EKQ
base-binding RM20A3 fragment antigen binding light chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
C

M
J

B
B

H
D

N
M

C
H

I
E

O
O

D
L

J
F

P
P

E
K

K
G

Q
Q

F
N

L
I

R
R

HIV-1 Env BG505 MD64 N332-GT5 SOSIP gp120

HIV-1 Env BG505 MD64 N332-GT5 SOSIP gp41

BG18-like precursor HMP1 fragment antigen binding heavy chain

BG18-like precursor HMP1 fragment antigen binding light chain

base-binding RM20A3 fragment antigen binding heavy chain

base-binding RM20A3 fragment antigen binding light chain

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