SMTL ID : 4yhz.1

Crystal structure of 304M3-B Fab in complex with H3K4me3 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-2-mer

Ligands

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: D.31, Y.32, Q.53, F.100, V.101, W.106 Chain D: F.100, V.101, R.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.53, A:V.101 Water bridges: A:Y.32, A:W.33 GOL.2: 6 residues within 4Å: Chain A: W.106 Chain C: K.4, T.6 Chain D: F.104, W.106 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.104 GOL.3: 5 residues within 4Å: Chain A: R.30, R.72, D.73, N.74, A.75 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.30, A:R.72, A:D.73, A:N.74, A:A.75 GOL.4: 4 residues within 4Å: Chain A: V.2, F.27, Y.32, R.98 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.32, A:R.98, A:R.98 Water bridges: A:T.28, A:D.109 GOL.5: 3 residues within 4Å: Chain A: G.15, R.16, S.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.17 GOL.6: 8 residues within 4Å: Chain B: Q.36, R.38, L.44, I.57, P.58, F.61, G.80, D.81 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.36, B:R.38, B:G.80 GOL.7: 4 residues within 4Å: Chain B: P.58, E.59, R.60, R.76 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.59, B:R.60, B:R.60, B:R.76 GOL.9: 9 residues within 4Å: Chain A: F.100, V.101, R.102 Chain D: D.31, Y.32, Q.53, F.100, V.101, W.106 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.53, D:V.101 Water bridges: D:Y.32, D:W.33 GOL.10: 6 residues within 4Å: Chain A: F.104, W.106 Chain D: W.106 Chain F: K.4, T.6 Ligands: GOL.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.104 GOL.11: 5 residues within 4Å: Chain D: R.30, R.72, D.73, N.74, A.75 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.30, D:R.72, D:N.74, D:A.75 GOL.12: 4 residues within 4Å: Chain D: V.2, F.27, Y.32, R.98 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.98, D:R.98 Water bridges: D:T.28, D:Y.32 GOL.13: 3 residues within 4Å: Chain D: G.15, R.16, S.17 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.17 GOL.14: 8 residues within 4Å: Chain E: Q.36, R.38, L.44, I.57, P.58, F.61, G.80, D.81 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.36, E:R.38, E:G.80, E:D.81 GOL.15: 4 residues within 4Å: Chain E: P.58, E.59, R.60, R.76 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.59, E:R.60, E:R.60, E:R.76

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

SO4.8: 4 residues within 4Å: Chain B: S.66, G.67, N.68, T.69 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.68, B:N.68, B:T.69 SO4.16: 4 residues within 4Å: Chain E: S.66, G.67, N.68, T.69 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.68, E:N.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hattori, T. et al., Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-02-10

Peptides

Fab Heavy Chain: AD
Fab Light Chain: BE
H3K4me3 peptide: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

D
H

B
L

E
L

C
P

F
P

Fab Heavy Chain

Fab Light Chain

H3K4me3 peptide

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