SMTL ID : 6okp.1

B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody 10-1074

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.28 Å

Oligo State

hetero-3-3-1-1-3-3-mer

Ligands

1 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.1: 11 residues within 4Å: Chain D: N.311, R.455 Chain I: Q.1, R.23, S.25, S.28, D.30, M.74, N.77 Ligands: NAG-NAG.4, NAG.44 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.23

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)-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-MAN-MAN-MAN.2: 20 residues within 4Å: Chain D: S.225, V.270, L.277, N.278, N.391, G.393, R.455, C.456, S.457, S.458 Chain I: V.51, D.54, G.55, S.56, Y.57, G.58, D.73, F.105, D.106, R.107 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.54 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.30: 21 residues within 4Å: Chain E: L.277, N.278, N.391, G.393, R.455, C.456, S.457, S.458 Chain K: V.51, Y.52, F.53, D.54, G.55, S.56, Y.57, G.58, D.73, F.105, D.106, R.107 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.12 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain K Hydrogen bonds: E:R.455, E:R.455, K:D.54 Hydrophobic interactions: K:Y.52, K:D.54 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.31: 22 residues within 4Å: Chain F: S.225, L.277, N.278, N.391, C.392, G.393, R.455, C.456, S.457, S.458 Chain M: V.51, Y.52, F.53, D.54, G.55, S.56, Y.57, G.58, D.73, F.105, D.106, R.107 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain M Hydrogen bonds: F:R.455, M:D.54 Hydrophobic interactions: M:Y.52, M:D.54

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.3: 11 residues within 4Å: Chain D: N.459 Chain I: I.104, F.105, D.106, T.109, Y.112, D.114 Chain J: S.30, V.32, A.33, S.92 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.12: 13 residues within 4Å: Chain E: N.278, L.281, N.459 Chain K: I.104, F.105, D.106, Y.112, D.114 Chain L: S.30, V.32, A.33, S.92 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.30 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:Y.112, K:Y.112 NAG-NAG-BMA-MAN-MAN-MAN-MAN.21: 11 residues within 4Å: Chain F: N.311, T.313, R.455 Chain M: R.23, G.27, S.28, D.30, M.74, N.77 Ligands: NAG-NAG.23, NAG.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.22: 12 residues within 4Å: Chain F: R.268, N.278, N.459 Chain M: I.104, F.105, D.106, T.109, Y.112, D.114 Chain N: V.32, A.33, S.92 No protein-ligand interaction detected (PLIP)

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.4: 5 residues within 4Å: Chain D: H.345, N.347, N.424, T.426 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain D: N.250, G.251, S.252, E.291 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain D: N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain D: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain D: N.165, Y.182, L.184, D.336 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.182 NAG-NAG.11: 7 residues within 4Å: Chain E: N.311, R.455 Chain K: S.28, D.30, N.77 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.19, NAG.53 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain E: N.250, G.251, S.252, S.290, E.291 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: I.374, N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain E: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain E: N.140, N.165, Y.182, L.184, D.336 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.182 NAG-NAG.23: 4 residues within 4Å: Chain F: H.345, N.347, T.426 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain F: N.250, G.251, S.252, S.290, E.291 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain F: N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain F: N.400, T.402, Q.428 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain F: N.165, Y.182, L.184, D.336 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.182

6 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.5: 3 residues within 4Å: Chain D: T.133, N.135, N.169 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 6 residues within 4Å: Chain D: K.350, P.403, N.406, D.416, Y.417, E.422 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.422, D:E.422 NAG-NAG-BMA.13: 2 residues within 4Å: Chain E: N.135, N.169 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 7 residues within 4Å: Chain E: K.350, P.403, N.406, D.416, G.421, E.422, I.425 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.422 Hydrogen bonds: E:K.350 NAG-NAG-BMA.24: 3 residues within 4Å: Chain F: T.133, N.135, N.169 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 7 residues within 4Å: Chain F: K.350, N.406, D.416, Y.417, G.420, G.421, E.422 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.420, F:E.422, F:E.422

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.19: 14 residues within 4Å: Chain E: N.311, T.313, H.345, N.347 Chain G: R.103, I.104, G.106, V.107, V.108 Chain H: N.45, N.46, P.61, D.62 Ligands: NAG-NAG.11 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:V.108

1 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.20: 14 residues within 4Å: Chain E: N.142 Chain G: Y.33, Y.50, S.52, R.54, E.55, S.56, A.57, R.100, F.114, Y.115 Chain H: D.90, G.94, F.95 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.56, G:A.57, G:Y.50

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

NAG.32: 1 residues within 4Å: Chain A: N.105 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: E.123, N.126 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.105 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: E.123, N.126 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.105 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: E.123, N.126 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain D: N.317, I.338, R.451 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: S.17 Chain D: N.93 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain D: N.245, N.257 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain D: N.292, T.294, D.295 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain D: K.350, N.354, Y.417, T.419 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain D: N.410, N.411 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain D: N.311, N.347, Q.423, N.424 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain D: P.369, N.370 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain D: R.208, N.213 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain E: N.317, I.338 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: G.92, N.93 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain E: N.245, N.257 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain E: N.292, T.294, D.295 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: K.350, N.354, T.419 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain E: N.410 Ligand excluded by PLIP NAG.53: 6 residues within 4Å: Chain E: N.311, N.347, S.349, Q.423, N.424 Ligands: NAG-NAG.11 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain E: P.369, N.370 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: R.208, N.213, T.214 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain F: N.317, I.338 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain C: S.17 Chain F: G.92, N.93 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain F: N.245, N.257 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain F: N.292, T.294, D.295 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain F: K.350, N.354, T.419 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain F: N.410, N.411 Ligand excluded by PLIP NAG.62: 5 residues within 4Å: Chain F: N.311, N.347, Q.423, N.424 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.21 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain F: P.369, N.370 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain D: I.174 Chain F: R.208, N.213 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schoofs, T. et al., Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope. Immunity (2019)

Release Date

2019-06-05

Peptides

Envelope glycoprotein gp41: ABC
Envelope glycoprotein gp120: DEF
10-1074 Heavy Chain,10-1074 Heavy Chain: G
10-1074 Light Chain,10-1074 Light Chain: H
SF12 Heavy Chain,SF12 Heavy Chain: IKM
SF12 Light Chain,SF12 Light Chain: JLN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
K

H
L

I
M

K
O

M
Q

J
N

L
P

N
R

Envelope glycoprotein gp41

Envelope glycoprotein gp120

10-1074 Heavy Chain,10-1074 Heavy Chain

10-1074 Light Chain,10-1074 Light Chain

SF12 Heavy Chain,SF12 Heavy Chain

SF12 Light Chain,SF12 Light Chain

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