SMTL ID : 8fbw.1 (1 other biounit)

Crystal structure of SIV-1 V2 antibody NCI05 in complex with a V2 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 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.1: 9 residues within 4Å: Chain A: T.100, Y.103, S.105, N.113 Chain B: S.31, N.32, Y.33, N.51, W.92 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.31, B:N.32, B:Y.33, A:S.105 Water bridges: B:W.92 Hydrophobic interactions: A:N.113

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 5 residues within 4Å: Chain A: T.57, Y.59, G.65, F.67, T.68 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.59 Hydrogen bonds: A:Y.59, A:Y.59, A:T.68, A:T.68 Water bridges: C:K.2 Salt bridges: C:K.2

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 2 residues within 4Å: Chain A: W.109 Chain C: W.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.102

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 5 residues within 4Å: Chain B: Q.38, K.46, L.48, P.60, F.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.38 Salt bridges: B:K.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stamos, J.D. et al., Effect of Passive Administration of Monoclonal Antibodies Recognizing Simian Immunodeficiency Virus (SIV) V2 in CH59-Like Coil/Helical or beta-Sheet Conformations on Time of SIV mac251 Acquisition. J.Virol. (2023)

Release Date

2023-01-18

Peptides

Heavy chain of anti-SIV V2 antibody NCI05: A
Light chain of anti-SIV V2 antibody NCI05: B
SIV V2 peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

Heavy chain of anti-SIV V2 antibody NCI05

Light chain of anti-SIV V2 antibody NCI05

SIV V2 peptide

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