SMTL ID : 3u7y.1

Structure of NIH45-46 Fab in complex with gp120 of 93TH057 HIV

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-1-1-1-mer

Ligands

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.1: 10 residues within 4Å: Chain B: K.91, S.93, D.95, V.138, N.146, N.244, R.246, C.306, V.307, S.308 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.91, B:K.91, B:R.246

1 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 6 residues within 4Å: Chain A: V.2, R.98, K.100, C.102, E.113, H.114 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.100 Water bridges: A:R.98, A:R.98, A:C.102 Salt bridges: A:R.98, A:R.98, A:H.114

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

NAG.3: 4 residues within 4Å: Chain B: T.239, M.240, N.253, T.255 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.253, B:T.255 NAG.4: 3 residues within 4Å: Chain B: N.179, Y.198, E.200 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.179, B:T.181, B:E.200 NAG.5: 6 residues within 4Å: Chain B: E.152, E.153, I.154, N.173, K.174, Q.212 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.174 Hydrogen bonds: B:I.154, B:N.173 NAG.7: 5 residues within 4Å: Chain B: N.118, T.120, I.156, L.161, H.220 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.161 Hydrogen bonds: B:N.118 NAG.8: 2 residues within 4Å: Chain B: E.44, N.45 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.44, B:E.44 NAG.9: 3 residues within 4Å: Chain C: I.20, S.63, N.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.63, C:S.63

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 6 residues within 4Å: Chain A: Y.107, Y.108, N.109 Chain B: N.163, A.165, K.166 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diskin, R. et al., Increasing the Potency and Breadth of an HIV Antibody by Using Structure-Based Rational Design. Science (2011)

Release Date

2011-11-16

Peptides

NIH45-46 heavy chain, Ig gamma-1 chain C region: A
Envelope glycoprotein gp160: B
NIH45-46 light chain, Ig kappa chain C region: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
G

C
L

NIH45-46 heavy chain, Ig gamma-1 chain C region

Envelope glycoprotein gp160

NIH45-46 light chain, Ig kappa chain C region

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