SMTL ID : 7sq1.1

BG505.MD39TS Env trimer in complex with Fab from antibody C05

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-2-2-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: 4 residues within 4Å: Chain B: N.102, R.112, K.116, Y.160 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: V.143, R.161, N.166, T.167 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.143 NAG-NAG.3: 3 residues within 4Å: Chain B: N.203, T.205, S.243 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain B: E.180, P.181, N.231, C.412, V.413, S.414 Ligands: BMA-MAN.5, NAG.40 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.270, T.272, I.291 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.300 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: T.340, T.341, N.354, S.356 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain D: T.104, N.117, Y.134, D.289 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain D: V.143, R.161, N.166, T.167 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain D: Q.262, N.264, N.300, S.302, R.411 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain D: T.266, H.298, N.300, T.382, R.411 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain D: N.323 Chain F: F.27, S.28, Y.32, Y.104 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Y.104 Hydrogen bonds: F:Y.104 NAG-NAG.16: 5 residues within 4Å: Chain D: T.340, T.341, N.354, R.386 Ligands: NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain D: S.356, N.360 Ligands: NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain D: N.366 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain H: N.102, R.112, G.113, K.116, Y.160 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain H: N.117 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain H: N.121 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 6 residues within 4Å: Chain H: R.318, N.323 Chain J: N.31, Y.32, Y.103, Y.104 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain H: T.341, N.354, S.356 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain H: G.232, L.234, P.260, N.415, T.417 No protein-ligand interaction detected (PLIP)

1 x BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose(Non-functional Binders)

BMA-MAN.5: 1 residues within 4Å: Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP)

3 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.11: 5 residues within 4Å: Chain D: N.203, T.205, P.207, S.243 Chain F: K.54 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.54 NAG-NAG-BMA.22: 4 residues within 4Å: Chain H: W.65, N.203, T.205, S.243 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 5 residues within 4Å: Chain H: E.180, P.181, N.231, C.346, V.413 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:V.413

1 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.12: 7 residues within 4Å: Chain D: E.180, L.230, N.231, C.412, V.413, S.414 Ligands: NAG.52 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.413

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

NAG.27: 3 residues within 4Å: Chain A: N.100, S.102, W.103 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.107 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.114 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.126, Y.127 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: E.56, N.57 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.105, N.106 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.117, L.136, D.289 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: S.119, F.120, N.121, K.132 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.245, T.247 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain B: Q.262, I.263, N.264, N.300, V.301, S.302 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.307 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: R.318, N.323 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.360 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: N.231, P.260, N.415 Ligands: NAG-NAG.4 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.100, S.102 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.107, E.110 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.114 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.126, Y.127 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain D: E.56, N.57 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain D: N.102, K.116, Y.160 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain D: N.106 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain D: F.120, N.121, K.132 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: N.245, T.247 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain D: N.270, I.291 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain D: K.303, N.307, T.367 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain D: P.260, N.415 Ligands: NAG-NAG-BMA-MAN.12 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain D: G.426, T.428, N.429 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain G: N.100, S.102 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain G: N.107, E.110 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain G: N.126 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain G: G.13, G.16, S.17 Chain H: E.56, N.57 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain H: N.105, N.106, I.290, G.292 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain H: R.161, N.166, T.167 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain H: N.245, T.247 Ligand excluded by PLIP NAG.61: 7 residues within 4Å: Chain H: Q.262, N.264, N.300, V.301, S.302, S.380, R.411 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain H: N.270, I.291, G.408 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain H: H.298, N.300, T.382 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain H: N.307, N.366, T.367 Ligand excluded by PLIP NAG.65: 1 residues within 4Å: Chain H: N.360 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain H: S.365, N.366 Chain J: Y.104 Ligand excluded by PLIP NAG.67: 4 residues within 4Å: Chain H: G.426, S.427, T.428, N.429 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Z. et al., Induction of tier-2 neutralizing antibodies in mice with a DNA-encoded HIV envelope native like trimer. Nat Commun (2022)

Release Date

2022-06-22

Peptides

Transmembrane protein gp41: ACG
Envelope glycoprotein gp160: BDH
C05 Fab Light chain: EI
C05 Fab heavy chain: FJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
D

G
F

B
C

D
E

H
G

E
L

I
I

F
H

J
A

Transmembrane protein gp41

Envelope glycoprotein gp160

C05 Fab Light chain

C05 Fab heavy chain

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