SMTL ID : 6udk.1

HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

7 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: 4 residues within 4Å: Chain A: V.144, R.162, N.167, T.168 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:S.99 NAG-NAG.5: 3 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: T.341, N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain C: V.144, R.162, N.167, T.168 Chain J: Y.48 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain C: T.342, N.355, S.357, R.387 Ligands: NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain C: N.246, T.248 Chain K: E.46, G.47, L.48, S.49 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.49

2 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.2: 8 residues within 4Å: Chain A: E.181, P.182, V.224, L.231, N.232, Q.408, V.414 Ligands: NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.12: 8 residues within 4Å: Chain C: E.181, P.182, V.224, L.231, N.232, N.346, V.414 Ligands: NAG.42 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.181

2 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: 5 residues within 4Å: Chain A: N.246, T.248 Chain M: E.46, G.47, L.48 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:E.46 NAG-NAG-BMA.8: 3 residues within 4Å: Chain B: N.246 Chain O: E.46, G.47 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:E.46

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN.4: 16 residues within 4Å: Chain A: T.267, H.299, N.301, S.381, V.383 Chain D: R.103, I.104, G.106, V.107, V.108 Chain E: S.25, N.45, Q.47, D.48, D.62, I.63 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.108 Hydrogen bonds: D:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.9: 14 residues within 4Å: Chain B: N.265, H.299, N.301, V.383 Chain F: R.103, I.104, G.106, V.107, V.108 Chain G: N.45, N.46, Q.47, D.62, I.63 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:V.108 Hydrogen bonds: F:V.108

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN.7: 8 residues within 4Å: Chain B: P.182, V.224, N.232, N.346, C.413, V.414, S.415 Ligands: NAG.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.181

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[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-MAN.13: 14 residues within 4Å: Chain C: T.267, H.299, N.301, V.383 Chain H: R.103, I.104, Y.105, G.106, V.107, V.108 Chain I: N.45, Q.47, D.62, I.63 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:V.108 Hydrogen bonds: H:G.106, H:R.103

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

NAG.16: 3 residues within 4Å: Chain A: Q.263, N.265, S.303 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.271, 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: 2 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.5 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.2 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: E.57, N.58 Chain P: S.17 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.204, T.206 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122, K.131 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.7 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: E.57, N.58 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.204, T.206, E.245 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: Q.263, N.265, S.303 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.271 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.308, W.364 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: G.323, N.324 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: S.357, N.361 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain B: Q.100, S.120, F.121, N.122, K.131 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: E.57, N.58 Chain R: S.17 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain C: Q.100, S.120, F.121, N.122, K.131 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.204, T.206 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: Q.263, N.265, S.303, V.414 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.271 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.308, S.362 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: S.357, N.361 Ligands: NAG-NAG.14 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.12 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schommers, P. et al., Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody. Cell (2020)

Release Date

2020-01-29

Peptides

RC1 variant of HIV-1 Env glycoprotein gp120: ABC
10-1074 Fab Heavy Chain: DFH
10-1074 Fab Light Chain: EGI
1-55 Fab Heavy Chain: JLN
1-55 Fab Light Chain: KMO
RC1 variant of HIV-1 Env glycoprotein gp41: PQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
K

C
R

D
A

F
F

H
O

E
B

G
I

I
P

J
M

L
D

N
H

K
N

M
E

O
L

P
C

Q
J

R
Q

RC1 variant of HIV-1 Env glycoprotein gp120

10-1074 Fab Heavy Chain

10-1074 Fab Light Chain

1-55 Fab Heavy Chain

1-55 Fab Light Chain

RC1 variant of HIV-1 Env glycoprotein gp41

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