SMTL ID : 4jdv.1 (1 other biounit)

Crystal structure of germ-line precursor of NIH45-46 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-mer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: R.67, R.85, R.87 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.87, A:R.87 Salt bridges: A:R.85, A:R.87 SO4.2: 2 residues within 4Å: Chain A: S.7, G.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.8 Water bridges: A:S.7, A:E.10 SO4.5: 2 residues within 4Å: Chain B: K.186, R.207 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.207 Salt bridges: B:K.186, B:R.207

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: F.178, P.179, V.181, S.189, L.190, S.191 Chain B: Q.156, S.158, S.172, S.173, T.174 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:F.178, A:S.191, B:S.158, B:T.174 Water bridges: A:S.189, B:T.174 GOL.6: 6 residues within 4Å: Chain A: V.175, H.176 Chain B: T.160, E.161, Q.162, D.163 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:V.175, B:E.161, B:D.163, B:D.163 Water bridges: A:T.177, A:T.177

1 x 144: TRIS-HYDROXYMETHYL-METHYL-AMMONIUM(Non-covalent)

144.4: 9 residues within 4Å: Chain A: Y.157, E.160, P.161, V.162, T.177, F.178, P.179, A.180, L.190 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.157, A:V.162 Salt bridges: A:E.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scharf, L. et al., Structural basis for HIV-1 gp120 recognition by a germ-line version of a broadly neutralizing antibody. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-03-20

Peptides

Fab heavy chain: A
Fab light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fab heavy chain

Fab light chain

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