SMTL ID : 6c5k.2 (1 other biounit)

S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 4 residues within 4Å: Chain A: R.38, S.40, K.43, N.88 No protein-ligand interaction detected (PLIP)

1 x GP1- Z9M- KDO- KDO- KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-8)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose

GP1-Z9M-KDO-KDO-KDO.2: 16 residues within 4Å: Chain A: T.31, Y.32, G.33, W.52, S.53, G.54, G.55, T.56, R.97, R.99, T.101 Chain B: H.31, K.32, N.33, Y.37, Y.101 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:K.32, B:K.32, A:T.31, A:G.33, A:R.99, B:N.33 Hydrophobic interactions: A:Y.32 Water bridges: A:R.97, A:R.97, A:R.97, A:R.99, A:T.101, B:Y.37 Salt bridges: A:R.97, A:R.99

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 4 residues within 4Å: Chain B: E.159, R.160, Q.161, N.162 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.161, B:N.162, B:N.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haji-Ghassemi, O. et al., Subtle Changes in the Combining Site of the Chlamydiaceae-Specific mAb S25-23 Increase the Antibody-Carbohydrate Binding Affinity by an Order of Magnitude. Biochemistry (2019)

Release Date

2019-01-09

Peptides

IgG1 Fab Heavy Chain: A
IgG1 Fab Light Chain (Kappa): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

IgG1 Fab Heavy Chain

IgG1 Fab Light Chain (Kappa)

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