SMTL ID : 5vn3.1

Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17b

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

12 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: 2 residues within 4Å: Chain C: N.250, S.252 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain C: E.309, N.311, N.347, S.349, R.455 Ligands: NAG-NAG-BMA.9, NAG-NAG-BMA.9, NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain C: H.345, N.347, N.424, T.426 Ligands: NAG-NAG-BMA.9, NAG-NAG-BMA.9 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain C: R.268, N.278, A.307, E.309, N.459 Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain H: N.250, S.252 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 9 residues within 4Å: Chain H: E.309, N.311, N.347, S.349, R.455, S.457 Ligands: NAG-NAG-BMA.20, NAG-NAG-BMA.20, NAG-NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain H: H.345, N.347, N.424, T.426 Ligands: NAG-NAG-BMA.20, NAG-NAG-BMA.20 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain H: N.278, A.307, E.309, N.459 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.14, NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain M: N.250, S.252 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 9 residues within 4Å: Chain M: E.309, N.311, N.347, S.349, R.455, S.457 Ligands: NAG-NAG-BMA.31, NAG-NAG-BMA.31, NAG-NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain M: N.347, N.424, T.426 Ligands: NAG-NAG-BMA.31, NAG-NAG-BMA.31 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 6 residues within 4Å: Chain M: N.278, A.307, E.309, N.459 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.25, NAG-NAG.27 No protein-ligand interaction detected (PLIP)

12 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.2: 4 residues within 4Å: Chain C: E.88, V.90, N.245, N.257 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 2 residues within 4Å: Chain C: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 7 residues within 4Å: Chain C: N.311, N.347, N.424, R.455 Ligands: NAG-NAG.5, NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 4 residues within 4Å: Chain C: P.403, N.406, D.415, D.416 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.416 NAG-NAG-BMA.13: 4 residues within 4Å: Chain H: E.88, V.90, N.245, N.257 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain H: T.387, N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 6 residues within 4Å: Chain H: N.347, N.424, R.455 Ligands: NAG-NAG.16, NAG-NAG.17, NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 4 residues within 4Å: Chain H: P.403, N.406, D.415, D.416 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.416 NAG-NAG-BMA.24: 4 residues within 4Å: Chain M: E.88, V.90, N.245, N.257 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 2 residues within 4Å: Chain M: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 6 residues within 4Å: Chain M: N.311, N.424, R.455 Ligands: NAG-NAG.27, NAG-NAG.28, NAG-NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 5 residues within 4Å: Chain M: K.350, P.403, N.406, D.415, D.416 2 PLIP interactions: 2 interactions with chain M Hydrophobic interactions: M:K.350 Hydrogen bonds: M:D.416

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.3: 14 residues within 4Å: Chain C: V.224, S.225, V.270, L.277, N.278, C.392, G.393, I.450, G.452, Q.453, R.455, C.456, S.457, S.458 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.14: 15 residues within 4Å: Chain H: V.224, S.225, P.228, V.270, L.277, N.278, N.391, C.392, G.393, I.450, G.452, Q.453, R.455, S.457 Ligands: NAG-NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.25: 14 residues within 4Å: Chain M: S.225, P.228, V.270, L.277, N.278, N.391, C.392, G.393, I.450, G.452, Q.453, R.455, S.457 Ligands: NAG-NAG.32 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: 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.4: 5 residues within 4Å: Chain C: N.292, I.293, T.294, D.295 Chain D: Q.33 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.15: 5 residues within 4Å: Chain H: N.292, I.293, T.294, D.295 Chain I: Q.33 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.26: 4 residues within 4Å: Chain M: N.292, I.293, T.294, D.295 No protein-ligand interaction detected (PLIP)

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.7: 2 residues within 4Å: Chain C: N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.18: 2 residues within 4Å: Chain H: N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.29: 2 residues within 4Å: Chain M: N.376, R.480 No protein-ligand interaction detected (PLIP)

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

NAG.34: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.105 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: D.113, N.114 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: D.125, N.126 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: S.17 Chain C: N.93 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: A.351, N.354, R.413 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: P.369, N.370 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.410, N.411 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain G: N.100, S.102 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain G: N.105 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain G: D.113, N.114 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain G: D.125, N.126 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain G: S.17 Chain H: N.93 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain H: A.351, N.354, R.413 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain H: P.369, N.370 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain H: N.410, N.411 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain L: N.100, S.102 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain L: N.105 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain L: D.113, N.114 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain L: D.125, N.126 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain L: S.17 Chain M: N.93 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain M: A.351, N.354, R.413 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain M: P.369, N.370 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain M: N.410, N.411 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ozorowski, G. et al., Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike. Nature (2017)

Release Date

2017-07-12

Peptides

17b Fab light chain: AFK
Envelope glycoprotein gp160: BGL
Envelope glycoprotein gp160: CHM
T-cell surface glycoprotein CD4: DIN
17b Fab heavy chain: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

F
N

K
O

B
A

G
B

L
D

C
G

H
I

M
J

D
C

I
E

N
F

E
H

J
K

O
M

17b Fab light chain

Envelope glycoprotein gp160

Envelope glycoprotein gp160

T-cell surface glycoprotein CD4

17b Fab heavy chain

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