SMTL ID : 5vn8.1

Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

21 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: 8 residues within 4Å: Chain A: C.131, R.208, C.212, N.213 Chain C: F.60, S.61, A.62, Q.65 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.250, S.252, P.254, S.290 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.292, T.294, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: E.309, N.311, N.347, I.348, S.349, N.424 Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain A: M.158, T.313, H.345, N.347, Q.423, N.424 Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain A: N.311, N.347, N.424 Ligands: NAG-NAG.6, NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain A: N.278, A.307, E.309, N.459 Ligands: NAG-NAG-BMA-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 8 residues within 4Å: Chain E: C.131, R.208, C.212, N.213 Chain G: F.60, S.61, A.62, Q.65 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain E: N.250, S.252, P.254, S.290 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: N.292, T.294, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain E: E.309, N.311, I.348, S.349 Ligands: NAG-NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 7 residues within 4Å: Chain E: M.158, T.313, H.345, N.347, Q.423, N.424 Ligands: NAG-NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain E: N.311, N.347, N.424 Ligands: NAG-NAG.17, NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain E: N.278, A.307, E.309, N.459 Ligands: NAG-NAG-BMA-MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 8 residues within 4Å: Chain I: C.131, R.208, C.212, N.213 Chain K: F.60, S.61, A.62, Q.65 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain I: N.250, S.252, P.254, S.290 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain I: N.292, T.294, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 7 residues within 4Å: Chain I: E.309, N.311, N.347, I.348, S.349, N.424 Ligands: NAG-NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 7 residues within 4Å: Chain I: M.158, T.313, H.345, N.347, Q.423, N.424 Ligands: NAG-NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 5 residues within 4Å: Chain I: N.311, N.347, N.424 Ligands: NAG-NAG.28, NAG-NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain I: N.278, A.307, E.309, N.459 Ligands: NAG-NAG-BMA-MAN.26 No protein-ligand interaction detected (PLIP)

9 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: E.88, V.90, N.245, N.257, S.259 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 2 residues within 4Å: Chain A: N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 6 residues within 4Å: Chain A: H.377, V.386, N.400, T.402 Chain C: S.103, W.104 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 5 residues within 4Å: Chain E: E.88, V.90, N.245, N.257, S.259 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 2 residues within 4Å: Chain E: N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 8 residues within 4Å: Chain E: H.377, V.386, N.400, T.402 Chain G: Y.102, S.103, W.104 Ligands: NAG.50 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 5 residues within 4Å: Chain I: E.88, V.90, N.245, N.257, S.259 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 2 residues within 4Å: Chain I: N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 8 residues within 4Å: Chain I: H.377, V.386, N.400, T.402 Chain K: Y.102, S.103, W.104 Ligands: NAG.61 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.4: 9 residues within 4Å: Chain A: V.270, L.277, N.278, N.391, G.393, R.455, S.457, S.458 Ligands: NAG-NAG.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.393 NAG-NAG-BMA-MAN.15: 8 residues within 4Å: Chain E: V.270, L.277, N.278, N.391, G.393, S.457, S.458 Ligands: NAG-NAG.22 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.225, E:G.393 NAG-NAG-BMA-MAN.26: 9 residues within 4Å: Chain I: V.270, L.277, N.278, N.391, G.393, R.455, S.457, S.458 Ligands: NAG-NAG.33 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.393

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

NAG.34: 1 residues within 4Å: Chain A: N.93 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: N.169, V.170, I.174 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain A: N.317, T.319, D.336, I.338 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: N.354, R.413, D.416, P.418 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: P.369, N.370 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: P.403, N.406, Y.417 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: T.372, N.410 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.100, S.102, W.103 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.105 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: E.110, D.113, N.114 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: K.122, D.125, N.126 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain E: N.93 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: N.169, V.170, I.174 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain E: N.317, T.319, D.336, I.338 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain E: N.354, R.413, D.416, P.418 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain E: P.369, N.370 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain E: P.403, N.406, Y.417 Ligands: NAG-NAG-BMA.20 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain E: T.372, N.410 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain F: N.105 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain F: E.110, D.113, N.114 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain F: K.122, D.125, N.126 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain I: N.93 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain I: N.169, V.170, I.174 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain I: N.317, T.319, D.336, I.338 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain I: N.354, R.413, D.416, P.418 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain I: P.369, N.370 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain I: P.403, N.406, Y.417 Ligands: NAG-NAG-BMA.31 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain I: T.372, N.410 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain J: N.100, S.102, W.103 Ligand excluded by PLIP NAG.64: 1 residues within 4Å: Chain J: N.105 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain J: E.110, D.113, N.114 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain J: K.122, D.125, N.126 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

Envelope glycoprotein gp160: AEI
Envelope glycoprotein gp160: BFJ
b12 Fab heavy chain: CGK
b12 Fab light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

E
D

I
E

B
A

F
B

J
C

C
H

G
F

K
I

D
L

H
J

L
K

Envelope glycoprotein gp160

Envelope glycoprotein gp160

b12 Fab heavy chain

b12 Fab light chain

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