SMTL ID : 8gpj.1

HIV-1 Env X16 UFO in complex with 8ANC195 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-6-mer

Ligands

4 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.1: 9 residues within 4Å: Chain E: S.109 Chain F: N.32, Y.50, R.51, A.53, A.54, L.55, A.67 Chain G: N.597 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.50, F:L.55 NAG-NAG-BMA.2: 7 residues within 4Å: Chain D: N.32, Y.50, R.51, A.53, A.54, L.55 Chain H: N.597 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.50, D:L.55 NAG-NAG-BMA.3: 7 residues within 4Å: Chain B: N.32, Y.50, R.51, A.53, A.54, L.55 Chain I: N.597 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.50, B:L.55 NAG-NAG-BMA.4: 4 residues within 4Å: Chain J: V.102, N.129, Y.146, D.293 No protein-ligand interaction detected (PLIP)

17 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.5: 3 residues within 4Å: Chain J: V.155, R.165, N.170 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain J: E.51, V.53, N.202, N.214 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:V.53 NAG-NAG.10: 6 residues within 4Å: Chain J: K.241, E.242, I.243, N.262, N.316, K.319 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:K.319, J:K.319 NAG-NAG.11: 3 residues within 4Å: Chain J: T.270, H.302, N.304 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain J: T.343, N.357, S.359 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain K: V.102, N.129, Y.146, L.148, D.293 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain K: V.155, R.165, N.170 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain K: E.51, N.202, N.214 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:E.51 NAG-NAG.19: 5 residues within 4Å: Chain K: K.241, E.242, N.262, N.316, K.319 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:K.319 NAG-NAG.20: 3 residues within 4Å: Chain K: T.270, H.302, N.304 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain K: T.343, N.357, S.359 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain L: N.103, N.129, Y.146, L.148, D.293 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain L: R.165, I.167, N.170, T.171 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:I.167 Hydrogen bonds: L:N.170 NAG-NAG.25: 4 residues within 4Å: Chain L: E.51, V.53, N.202, N.214 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:V.53 NAG-NAG.28: 6 residues within 4Å: Chain L: K.241, E.242, I.243, N.262, N.316, K.319 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:K.319 NAG-NAG.29: 5 residues within 4Å: Chain L: T.270, H.302, N.304, T.380, T.382 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain L: T.343, N.357, S.359 Ligands: NAG.50 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- 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-(1-6)-[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-MAN-MAN-MAN.6: 21 residues within 4Å: Chain C: 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, L.74, I.81, S.83, E.85 Chain J: R.205, N.207, H.324 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.71, C:D.73 Hydrophobic interactions: C:W.55 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.15: 19 residues within 4Å: Chain E: T.19, W.55, S.57, S.58, A.59, R.64, G.65, V.67, L.68, S.70, A.71, V.72, D.73, L.74, P.80, S.83, E.85 Chain K: N.207, H.324 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:A.71, E:D.73, E:D.73

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.8: 9 residues within 4Å: Chain J: V.227, L.234, N.235, N.348, R.350, C.412, K.413, S.414 Ligands: NAG.37 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:R.350, J:K.413 NAG-NAG-BMA-MAN-MAN.17: 11 residues within 4Å: Chain K: D.184, P.185, V.227, L.234, N.235, N.348, R.350, C.412, K.413, S.414 Ligands: NAG.46 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:D.184, K:K.413 NAG-NAG-BMA-MAN-MAN.26: 10 residues within 4Å: Chain L: D.184, P.185, V.227, L.234, N.235, N.348, R.350, K.413, S.414 Ligands: NAG.52 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:R.350, L:K.413 Hydrophobic interactions: L:K.413

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.9: 8 residues within 4Å: Chain C: Q.1, H.3, V.5, Y.25, G.26 Chain J: N.249, T.251, N.252 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.1 NAG-NAG-BMA-MAN.18: 10 residues within 4Å: Chain E: Q.1, H.3, Y.25, G.26, V.27, N.28, S.78 Chain K: N.249, T.251, N.252 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.1 NAG-NAG-BMA-MAN.27: 8 residues within 4Å: Chain A: Q.1, H.3, Y.25, G.26, N.28 Chain L: N.249, T.251, N.252 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.25 Hydrogen bonds: A:Q.1

1 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.24: 17 residues within 4Å: Chain A: T.19, W.55, S.57, A.59, F.63, R.64, V.67, L.68, I.69, S.70, A.71, V.72, D.73, I.81, E.85 Chain L: N.207, H.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.71, A:D.73, A:D.73, A:S.57, A:R.64, A:I.69

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

NAG.31: 3 residues within 4Å: Chain F: S.28 Chain G: S.572, N.576 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain G: N.584, N.585 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain D: S.28 Chain H: S.572, N.576 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: S.28 Chain I: S.572, N.576 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain H: S.501 Chain J: E.55, N.56 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain J: T.96, S.131, F.132, N.133, K.144 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain J: N.235, S.264, N.415 Ligands: NAG-NAG-BMA-MAN-MAN.8 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain J: N.274, I.295 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain J: S.359, N.363 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain J: R.350, N.409, T.411 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain G: S.501 Chain K: E.55, N.56 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain K: T.96, D.98, S.131, F.132, N.133, K.144 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain K: N.274, I.295 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain K: N.363 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain K: N.409, T.411 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain K: N.235, S.264, N.415 Ligands: NAG-NAG-BMA-MAN-MAN.17 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain I: S.501 Chain L: E.55, N.56 Ligand excluded by PLIP NAG.48: 6 residues within 4Å: Chain L: T.96, D.98, S.131, F.132, N.133, K.144 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain L: N.274, I.295 Ligands: NAG.51 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain L: S.359, N.363 Ligands: NAG-NAG.30 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain L: N.409, T.411 Ligands: NAG.49 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain L: N.235, S.264, N.415 Ligands: NAG-NAG-BMA-MAN-MAN.26 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
X16 UFO gp41: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

E
H

B
C

D
E

F
L

G
U

H
V

I
W

J
X

K
Y

L
Z

8ANC195 Fab heavy chain

8ANC195 Fab light chain

X16 UFO gp41

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