SMTL ID : 8tca.1

Structure of a mouse IgG antibody antigen-binding fragment (Fab) targeting N6-methyladenosine (m6A), an RNA modification, no ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: T.93, T.115, V.116, F.151, L.175, Y.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.90, A:Y.180 EDO.2: 6 residues within 4Å: Chain A: F.29, S.74, D.75, K.76, R.79, S.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.79, A:R.79, A:S.80, A:S.80 Water bridges: A:K.76 EDO.3: 5 residues within 4Å: Chain A: Q.39, P.41, G.94, I.95, L.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.39, A:Y.180, A:Y.180 EDO.4: 4 residues within 4Å: Chain A: V.2, K.3, L.4, W.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.4, A:L.4 Water bridges: A:W.108, A:W.108 EDO.5: 2 residues within 4Å: Chain A: A.119, K.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.120 Water bridges: A:K.120, A:T.122 EDO.6: 7 residues within 4Å: Chain B: Q.39, K.41, P.61, R.63, F.64, D.83, D.84 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.39, B:K.41, B:D.83, B:D.84 EDO.7: 3 residues within 4Å: Chain B: L.109, P.144, E.201 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.201 EDO.8: 3 residues within 4Å: Chain B: K.105, S.168, K.169 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.105, B:K.169 Water bridges: B:P.167 EDO.9: 4 residues within 4Å: Chain B: N.131, A.185, R.186, E.189 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.189 Water bridges: B:R.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Angelo, M.C. et al., Structure of a mouse IgG antibody antigen-binding fragment (Fab) targeting N6-methyladenosine (m6A), an RNA modification. To Be Published

Release Date

2024-02-07

Peptides

m6A binding IgG Fab, heavy chain: A
m6A binding IgG Fab, light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

m6A binding IgG Fab, heavy chain

m6A binding IgG Fab, light chain

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