SMTL ID : 6c5h.1

S25-5 Fab in complex with Chlamydiaceae-specific LPS antigen

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 4 residues within 4Å: Chain A: K.43, Q.86, P.87, N.88 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.43, A:K.43, A:K.43 Hydrogen bonds: A:N.88

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, S.56, R.97, R.99, T.101, T.102 Chain B: H.31, N.33, Y.37, Y.101 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.32 Hydrogen bonds: A:T.31, A:G.33, B:N.33 Water bridges: A:T.31, A:Y.32, A:R.97, A:R.97, A:R.99, A:T.101, A:T.101, A:T.102, B:Y.37 Salt bridges: A:R.97, A:R.99

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 7 residues within 4Å: Chain A: P.87, T.90, S.117, F.151, L.175, D.178, Y.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.90

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

PEG.4: 6 residues within 4Å: Chain A: Q.39, S.40, P.41, T.90, V.92, L.113 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.40 PEG.5: 3 residues within 4Å: Chain A: V.92, Q.110, G.111 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.113

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.6: 8 residues within 4Å: Chain A: E.153, P.154, V.155, T.170, F.171, P.172, A.173, L.182 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.170, A:L.182 Hydrogen bonds: A:E.153, A:E.153, A:V.155, A:A.173

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

CL.7: 3 residues within 4Å: Chain B: L.15, E.84, A.85 Ligand excluded by PLIP

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Fab Heavy Chain (IgG1)

Fab Light Chain (IgG1 Kappa)

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