SMTL ID : 3tv3.1

Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with Man9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 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-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose

MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: G.90, N.91, W.92, D.93 Chain B: W.60, N.61, W.64, T.65, Y.66, H.67, P.69, K.72, W.116 Ligands: AML.3 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: T.161, T.162 Chain B: P.43, G.44, P.189, A.190, V.191, L.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.162, A:T.162 GOL.4: 4 residues within 4Å: Chain B: T.76, L.77, A.78 Ligands: EPE.7 No protein-ligand interaction detected (PLIP) GOL.5: 7 residues within 4Å: Chain A: L.43, Y.46, P.52 Chain B: R.105, G.107, W.121, D.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.121, B:D.123 GOL.6: 6 residues within 4Å: Chain B: L.11, T.132, F.168, P.169, E.170, Y.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.170

1 x AML: AMYLAMINE(Non-covalent)

AML.3: 2 residues within 4Å: Chain B: W.60 Ligands: MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.60

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.7: 8 residues within 4Å: Chain B: L.53, H.55, R.62, T.65, H.67, T.76, L.77 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.77 Salt bridges: B:H.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pejchal, R. et al., A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield. Science (2011)

Release Date

2011-10-19

Peptides

PGT128 light chain, Ig lambda-2 chain C regions: A
PGT128 heavy chain, Ig gamma-1 chain C region: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

PGT128 light chain, Ig lambda-2 chain C regions

PGT128 heavy chain, Ig gamma-1 chain C region

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