SMTL ID : 5gir.2 (1 other biounit)

Crystal structure of a Fab fragment with its ligand peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.78 Chain B: S.113, W.114 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.114 Salt bridges: A:R.78 SO4.2: 3 residues within 4Å: Chain A: S.139 Ligands: EDO.3, EDO.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:A.137, A:A.137, A:S.139 Hydrogen bonds: B:E.143 SO4.5: 2 residues within 4Å: Chain B: Q.47, R.48 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.48 Water bridges: B:S.46

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: P.138, S.139, V.140, V.225 Ligands: SO4.2, EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.140 EDO.4: 6 residues within 4Å: Chain A: A.137, P.138, T.223, V.225 Ligands: SO4.2, EDO.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kitago, Y. et al., Structural basis for multi-specific peptide recognition by the anti-IDH1/2 monoclonal antibody, MsMab-1. Biochem. Biophys. Res. Commun. (2016)

Release Date

2016-09-14

Peptides

Heavy chain of Fab fragment: A
Light chain of Fab fragment: B
LYS-PRO-ILE-ILE-ILE-GLY-SER-HIS-ALA-TYR-GLY-ASP: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Heavy chain of Fab fragment

Light chain of Fab fragment

LYS-PRO-ILE-ILE-ILE-GLY-SER-HIS-ALA-TYR-GLY-ASP

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