SMTL ID : 8gje.1

HIV-1 Env subtype C CZA97.12 SOSIP.664 in complex with 3BNC117 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

18 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: 5 residues within 4Å: Chain A: T.140, F.141, N.155, Y.172, D.324 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.172 NAG-NAG.2: 4 residues within 4Å: Chain A: T.133, H.135, N.159, Q.170 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: E.88, V.90, N.233, N.245, S.247 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.90 NAG-NAG.7: 3 residues within 4Å: Chain A: V.299, Y.333, N.335 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: T.375, N.389, T.391 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain E: T.140, F.141, N.155, Y.172, D.324 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.172 NAG-NAG.11: 4 residues within 4Å: Chain E: T.133, H.135, N.159, Q.170 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain E: N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain E: E.88, V.90, N.233, N.245, S.247 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.90 NAG-NAG.16: 3 residues within 4Å: Chain E: V.299, Y.333, N.335 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain E: T.375, N.389, T.391 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain I: T.140, F.141, N.155, Y.172, D.324 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.172 NAG-NAG.20: 4 residues within 4Å: Chain I: T.133, H.135, N.159, Q.170 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain I: N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain I: E.88, V.90, N.233, N.245, S.247 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:V.90 NAG-NAG.25: 3 residues within 4Å: Chain I: V.299, Y.333, N.335 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain I: T.375, N.389, T.391 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.3: 8 residues within 4Å: Chain A: V.181, L.182, L.183, N.201, A.202 Chain C: W.76 Chain E: E.163, R.312 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.181 Hydrogen bonds: A:L.182 NAG-NAG-BMA-FUC.12: 8 residues within 4Å: Chain E: V.181, L.182, L.183, N.201, A.202 Chain G: W.76 Chain I: E.163, R.312 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.181 Hydrogen bonds: E:L.182 NAG-NAG-BMA-FUC.21: 8 residues within 4Å: Chain A: E.163, R.312 Chain I: V.181, L.182, L.183, N.201, A.202 Chain K: W.76 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:V.181 Hydrogen bonds: I:L.182

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[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.6: 17 residues within 4Å: Chain A: V.70, P.210, K.211, V.212, N.213, F.214, D.215, V.258, L.265, N.266, R.308, N.380, R.382, I.429, K.436, S.437 Ligands: NAG.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.382, A:R.382 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.15: 17 residues within 4Å: Chain E: V.70, P.210, K.211, V.212, N.213, F.214, D.215, V.258, L.265, N.266, R.308, N.380, R.382, I.429, K.436, S.437 Ligands: NAG.45 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.382, E:R.382 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24: 17 residues within 4Å: Chain I: V.70, P.210, K.211, V.212, N.213, F.214, D.215, V.258, L.265, N.266, R.308, N.380, R.382, I.429, K.436, S.437 Ligands: NAG.56 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.382, I:R.382

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.9: 8 residues within 4Å: Chain A: E.279, N.280 Chain D: G.27, Y.28, R.62, W.63, G.64, Y.87 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.28 NAG-NAG-BMA-MAN-MAN-MAN-MAN.18: 8 residues within 4Å: Chain E: E.279, N.280 Chain H: G.27, Y.28, R.62, W.63, G.64, Y.87 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:Y.28 NAG-NAG-BMA-MAN-MAN-MAN-MAN.27: 8 residues within 4Å: Chain I: E.279, N.280 Chain L: G.27, Y.28, R.62, W.63, G.64, Y.87 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:Y.28

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

NAG.28: 3 residues within 4Å: Chain A: E.92, N.93 Chain B: S.17 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.138, K.151, N.191 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: K.272, E.273, N.293, R.347, K.351 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: N.305, T.307, G.431 Ligands: NAG.33 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: N.342, K.346, A.398, T.399 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.432, T.434 Ligands: NAG.31 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: S.295, N.438 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: D.110, N.114 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: R.122, E.123, N.126 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain D: R.61, R.62, W.63, E.66, N.68 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain E: E.92, N.93 Chain F: S.17 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain E: N.138, K.151, N.191 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain E: K.272, E.273, N.293, R.347, K.351 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain E: N.305, T.307, G.431 Ligands: NAG.44 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain E: N.342, K.346, A.398, T.399 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain E: N.432, T.434 Ligands: NAG.42 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: S.295, N.438 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.15 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain F: D.110, N.114 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain F: R.122, E.123, N.126 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain H: R.61, R.62, W.63, E.66, N.68 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain I: E.92, N.93 Chain J: S.17 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain I: N.138, K.151, N.191 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain I: K.272, E.273, N.293, R.347, K.351 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain I: N.305, T.307, G.431 Ligands: NAG.55 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain I: N.342, K.346, A.398, T.399 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain I: N.432, T.434 Ligands: NAG.53 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain I: S.295, N.438 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain J: N.100, S.102 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain J: D.110, N.114 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain J: R.122, E.123, N.126 Ligand excluded by PLIP NAG.60: 5 residues within 4Å: Chain L: R.61, R.62, W.63, E.66, N.68 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ringe, R.P. et al., Glycan heterogeneity as a cause of the persistent fraction in HIV-1 neutralization. Plos Pathog. (2023)

Release Date

2023-10-18

Peptides

CZA97.12 SOSIP.664 Envelope glycoprotein gp120: AEI
CZA97.12 SOSIP.664 Envelope glycoprotein gp41: BFJ
3BNC117 Fab heavy chain: CGK
3BNC117 kappa light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

I
D

B
B

F
E

J
F

C
H

G
G

K
I

D
L

H
J

L
K

CZA97.12 SOSIP.664 Envelope glycoprotein gp120

CZA97.12 SOSIP.664 Envelope glycoprotein gp41

3BNC117 Fab heavy chain

3BNC117 kappa light chain

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