SMTL ID : 2v83.1

Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-trimer

Ligands

2 x ALA- ARG- THR- M3L- GLN- THR- ALA- ARG- LYS: HISTONE H3(Non-covalent)

ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-LYS.1: 25 residues within 4Å: Chain A: Y.10, S.30, T.31, E.32, K.35, P.36, A.37, M.38, I.39, Y.40, W.48, L.61, L.64, S.65, E.66, G.67, S.68, N.69, Y.71 Chain B: G.44, D.45 Chain C: W.11, I.22, N.23, W.25 31 PLIP interactions: 23 interactions with chain A, 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:Y.10, A:K.35, A:I.39, A:W.48, A:L.61, A:Y.71, C:I.22 Hydrogen bonds: A:Y.10, A:Y.10, A:T.31, A:E.32, A:M.38, A:M.38, A:Y.40, A:L.64, C:W.11, C:N.23 Water bridges: A:K.35, A:Y.40, A:S.65, A:S.65, A:N.69, C:W.11, C:W.11, C:N.23, C:N.23 Salt bridges: A:E.66, B:D.45 pi-Cation interactions: A:Y.10, A:W.48, A:W.48 ALA-ARG-THR-M3L-GLN-THR-ALA-ARG-LYS.2: 22 residues within 4Å: Chain B: F.8, G.9, Y.10, S.30, T.31, E.32, L.33, K.35, P.36, A.37, M.38, I.39, Y.40, W.48, L.61, I.62, L.64, S.65, G.67, S.68, N.69, Y.71 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:K.35, B:I.39, B:W.48, B:W.48, B:Y.71 Hydrogen bonds: B:Y.10, B:T.31, B:T.31, B:M.38, B:M.38, B:Y.40, B:N.69 Water bridges: B:E.32, B:N.34, B:S.65 pi-Cation interactions: B:Y.10, B:W.48, B:W.48

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.14, C.18, V.20, H.50, C.53 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.14, A:C.18, A:H.50, A:C.53 ZN.4: 4 residues within 4Å: Chain A: C.41, H.47, C.73, H.76 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.41, A:H.47, A:C.73, A:H.76 ZN.5: 5 residues within 4Å: Chain B: C.14, C.18, V.20, H.50, C.53 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.14, B:C.18, B:H.50, B:C.53 ZN.6: 4 residues within 4Å: Chain B: C.41, H.47, C.73, H.76 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.41, B:H.47, B:C.73, B:H.76 ZN.7: 5 residues within 4Å: Chain C: C.14, C.18, V.20, H.50, C.53 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.14, C:C.18, C:H.50, C:C.53 ZN.8: 4 residues within 4Å: Chain C: C.41, H.47, C.73, H.76 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.41, C:H.47, C:C.73, C:H.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramon-Maiques, S. et al., The Plant Homeodomain Finger of Rag2 Recognizes Histone H3 Methylated at Both Lysine-4 and Arginine-2. Proc.Natl.Acad.Sci.USA (2007)

Release Date

2007-12-11

Peptides

VDJ RECOMBINATION-ACTIVATING PROTEIN 2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

VDJ RECOMBINATION-ACTIVATING PROTEIN 2

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