SMTL ID : 4jm2.1

Crystal Structure of PGT 135 Fab in Complex with gp120 Core Protein from HIV-1 Strain JR-FL Bound to CD4 and 17b Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: 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(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: T.64, H.65, R.71, L.113, V.114, I.116 Chain B: E.92, E.93, W.94, R.96 Chain E: H.164, N.166, T.242, T.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.64, A:Y.66, A:R.71, A:R.71, A:L.113, A:V.114 Hydrophobic interactions: A:V.114

1 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.2: 22 residues within 4Å: Chain A: R.104, R.106, H.108, D.109, V.110, W.119, D.121 Chain B: F.49, Y.52, S.53, K.54, I.55, A.56, F.62, V.63, A.64 Chain E: Q.222, N.225, N.236, N.237, E.239 Ligands: NAG-NAG-BMA.3 8 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A, 1 interactions with chain E Hydrogen bonds: B:K.54, A:R.104, A:R.106, A:R.106, A:W.119, A:D.121, A:D.121, E:E.239

1 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: W.34, K.37 Chain E: N.219, T.221 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:T.221 Hydrogen bonds: A:K.37

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 2 residues within 4Å: Chain C: T.56 Chain D: K.116 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.100

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

NAG.5: 7 residues within 4Å: Chain E: V.102, N.110, N.210, C.274, S.275, S.276 Ligands: NAG.7 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.110, E:S.276 NAG.6: 3 residues within 4Å: Chain E: V.193, N.195, R.298 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:V.193 Hydrogen bonds: E:N.195, E:R.298, E:R.298 NAG.7: 6 residues within 4Å: Chain E: N.110, S.139, S.275, S.276, N.277 Ligands: NAG.5 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.139, E:N.277 NAG.8: 4 residues within 4Å: Chain E: N.173, W.228, E.233, S.235 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.228 Hydrogen bonds: E:N.173, E:E.233, E:S.235, E:S.235 NAG.9: 3 residues within 4Å: Chain E: N.124, T.126, N.127 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:T.126, E:N.127 Hydrogen bonds: E:N.127, F:Q.33 NAG.10: 4 residues within 4Å: Chain E: E.141, N.143, N.166, S.275 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.143, E:R.273, E:S.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kong, L. et al., Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120. Nat.Struct.Mol.Biol. (2013)

Release Date

2013-05-29

Peptides

PGT 135 Heavy chain: A
PGT 135 Light chain: B
17b Light chain: C
17b Heavy chain: D
gp120: E
T-cell surface glycoprotein CD4: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

PGT 135 Heavy chain

PGT 135 Light chain

17b Light chain

17b Heavy chain

gp120

T-cell surface glycoprotein CD4

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