SMTL ID : 8gpi.1

HIV-1 Env X18 UFO in complex with 8ANC195 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-6-mer

Ligands

23 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: 10 residues within 4Å: Chain C: W.108, S.109 Chain D: N.32, Y.50, R.51, A.53, A.54, L.55 Chain G: S.594, N.595 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.50, D:L.55 NAG-NAG.2: 8 residues within 4Å: Chain E: W.108 Chain F: N.32, Y.50, R.51, A.53, A.54 Chain H: S.594, N.595 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.50 NAG-NAG.3: 7 residues within 4Å: Chain A: W.108 Chain B: N.32, Y.50, R.51, A.53, A.54 Chain I: N.595 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.50 NAG-NAG.4: 6 residues within 4Å: Chain J: A.102, N.103, N.133, T.135, L.152, D.297 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain J: V.159, R.169, I.171, N.174 Chain K: R.285 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain J: T.274, E.308, N.409 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain J: N.360, T.362, N.366 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:T.362 NAG-NAG.11: 6 residues within 4Å: Chain J: E.245, E.246, I.247, N.266, K.320, E.323 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:E.323 NAG-NAG.12: 3 residues within 4Å: Chain J: N.315, N.319, F.375 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain J: N.98 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain K: N.103, N.133 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain K: R.169, N.174 Chain L: R.285 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain K: E.245, E.246, I.247, N.266, K.320, E.323 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:K.320, K:E.323 NAG-NAG.20: 4 residues within 4Å: Chain K: M.347, N.360, T.362, N.366 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:T.362 NAG-NAG.21: 5 residues within 4Å: Chain K: S.272, T.274, Y.306, E.308, N.409 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain K: N.98, E.167 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain L: A.102, N.103, N.133, L.152, D.297 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain J: R.285 Chain L: R.169, N.174, D.342 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 6 residues within 4Å: Chain L: E.245, E.246, I.247, N.266, K.320, E.323 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:K.320, L:E.323 NAG-NAG.29: 3 residues within 4Å: Chain L: N.315, N.319, N.376 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain L: M.347, N.360, T.362, R.384 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:T.362 NAG-NAG.31: 5 residues within 4Å: Chain L: S.272, T.274, Y.306, E.308, N.409 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 1 residues within 4Å: Chain L: N.98 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN-MAN.6: 19 residues within 4Å: Chain C: T.19, W.55, S.57, A.59, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.83, E.85 Chain J: K.209, N.211, H.328 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.73, C:A.71, C:S.57, C:A.59, C:G.65, C:I.69, C:I.69 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.16: 19 residues within 4Å: Chain E: T.19, W.55, S.57, S.58, A.59, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, E.85 Chain K: K.209, N.211, H.328 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.73, E:A.71, E:A.59, E:G.65, E:I.69, E:I.69 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.25: 20 residues within 4Å: Chain A: T.19, W.55, S.57, S.58, A.59, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.83, E.85 Chain L: K.209, N.211, H.328 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.73, A:A.71, A:A.59, A:G.65, A:I.69, A:I.69

3 x NAG- NAG- BMA- MAN- MAN: 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.7: 9 residues within 4Å: Chain J: D.188, L.238, N.239, N.351, R.353, C.410, T.411, S.412 Ligands: NAG.41 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:R.353, J:T.411 NAG-NAG-BMA-MAN-MAN.17: 11 residues within 4Å: Chain K: P.189, V.231, L.238, N.239, N.351, C.352, R.353, C.410, T.411, S.412 Ligands: NAG.52 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:R.353, K:T.411 NAG-NAG-BMA-MAN-MAN.26: 10 residues within 4Å: Chain L: D.188, L.238, N.239, N.351, C.352, R.353, C.410, T.411, S.412 Ligands: NAG.58 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:R.353, L:T.411

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.10: 7 residues within 4Å: Chain C: Q.1, H.3, Y.25, G.26 Chain J: N.253, T.255, N.256 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.1 NAG-NAG-BMA.18: 7 residues within 4Å: Chain E: Q.1, H.3, Y.25, G.26 Chain K: N.253, T.255, N.256 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.1 NAG-NAG-BMA.27: 7 residues within 4Å: Chain A: Q.1, H.3, Y.25, G.26 Chain L: N.253, T.255, N.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.1

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

NAG.33: 2 residues within 4Å: Chain G: N.569, T.571 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain H: N.569 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain I: N.569 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain G: S.499 Chain J: E.55, N.56 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain J: N.103, H.106 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain J: N.126, R.303, K.304, Y.306, I.380 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain J: N.137, Q.146 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain J: N.206, N.218 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain J: N.239, S.268, N.413 Ligands: NAG-NAG-BMA-MAN-MAN.7 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain J: N.278, I.299 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain J: N.310, E.313, T.378 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain H: S.499 Chain K: E.55, N.56 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain K: N.103 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain K: N.126, T.128 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain K: N.137 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain K: N.206, N.218 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain K: N.278, I.299, I.407 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain K: N.310, T.312, E.313, T.378 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain K: N.315, N.319, E.374, F.375, N.376 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain K: N.239, S.268, N.413 Ligands: NAG-NAG-BMA-MAN-MAN.17 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain I: S.499 Chain L: E.55, N.56 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain L: N.103, H.106 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain L: T.105, N.126, T.128, I.302 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain L: N.137 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain L: N.206, N.218 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain L: N.239, S.268, N.413 Ligands: NAG-NAG-BMA-MAN-MAN.26 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain L: N.278, I.299, I.407 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain L: N.310, T.312, E.313, T.378 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain L: N.330 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niu, J. et al., Structures and immune recognition of Env trimers from two Asia prevalent HIV-1 CRFs. Nat Commun (2023)

Release Date

2023-08-09

Peptides

8ANC195 Fab heavy chain: ACE
8ANC195 Fab light chain: BDF
X18 UFO gp41: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

E
H

B
C

D
E

F
L

G
R

H
S

I
T

J
X

K
Y

L
Z

8ANC195 Fab heavy chain

8ANC195 Fab light chain

X18 UFO gp41

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