SMTL ID : 4fl6.1

Crystal structure of the complex of the 3-MBT repeat domain of L3MBTL3 and UNC1215

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 x UWN: [2-(phenylamino)benzene-1,4-diyl]bis{[4-(pyrrolidin-1-yl)piperidin-1-yl]methanone}(Non-covalent)

UWN.1: 17 residues within 4Å: Chain A: D.154, N.157, F.160, C.162, F.178, W.181, Y.185 Chain B: D.47, H.50, V.53, F.71, Y.74, Y.78, H.103, D.182, E.183, S.184 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.160, A:F.160, A:F.178, A:F.178, A:W.181, A:W.181, A:Y.185, A:Y.185, B:V.53, B:F.71, B:Y.74, B:Y.74, B:Y.78 Salt bridges: A:D.154, B:D.47 pi-Cation interactions: A:W.181, A:W.181 UWN.2: 18 residues within 4Å: Chain A: D.47, H.50, V.53, F.71, Y.74, Y.78, H.103, D.182, E.183, S.184 Chain B: D.154, N.157, F.160, C.162, F.178, W.181, Y.185 Ligands: UNX.19 18 PLIP interactions: 7 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:V.53, A:F.71, A:Y.74, A:Y.74, A:Y.78, A:Y.78, B:F.160, B:F.160, B:F.160, B:F.178, B:F.178, B:W.181, B:Y.185, B:Y.185 Salt bridges: A:D.47, B:D.154 pi-Cation interactions: B:W.181, B:W.181

29 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 1 residues within 4Å: Chain A: D.88 Ligand excluded by PLIP UNX.4: 3 residues within 4Å: Chain A: Y.74, S.75, Y.78 Ligand excluded by PLIP UNX.5: 1 residues within 4Å: Chain A: K.156 Ligand excluded by PLIP UNX.6: 4 residues within 4Å: Chain A: V.163, D.179, W.181, P.212 Ligand excluded by PLIP UNX.7: 2 residues within 4Å: Chain A: K.149, T.230 Ligand excluded by PLIP UNX.8: 4 residues within 4Å: Chain A: V.153, I.161, P.194, H.197 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: N.180 Chain B: N.180 Ligand excluded by PLIP UNX.10: 1 residues within 4Å: Chain A: D.224 Ligand excluded by PLIP UNX.11: 4 residues within 4Å: Chain A: H.27, N.83, D.85, P.298 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain A: A.86, L.87 Ligand excluded by PLIP UNX.13: 4 residues within 4Å: Chain A: N.35, G.64, Y.65, T.309 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: H.50 Chain B: K.156, N.157 Ligand excluded by PLIP UNX.15: 6 residues within 4Å: Chain A: E.49, H.50, Q.51, E.183, S.184, D.186 Ligand excluded by PLIP UNX.16: 6 residues within 4Å: Chain A: S.52, T.167, L.175, H.177, E.183, D.186 Ligand excluded by PLIP UNX.17: 5 residues within 4Å: Chain A: V.56, F.71, D.72, Y.74, P.105 Ligand excluded by PLIP UNX.18: 6 residues within 4Å: Chain A: H.70, F.71, S.75, D.76, Y.78, D.79 Ligand excluded by PLIP UNX.19: 4 residues within 4Å: Chain A: D.47, E.49, F.71 Ligands: UWN.2 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain A: A.86, I.89, F.132 Ligand excluded by PLIP UNX.21: 4 residues within 4Å: Chain A: G.147, M.148, S.232, L.233 Ligand excluded by PLIP UNX.22: 3 residues within 4Å: Chain A: H.177, D.179, N.180 Ligand excluded by PLIP UNX.23: 3 residues within 4Å: Chain A: R.173, C.189, E.190 Ligand excluded by PLIP UNX.24: 5 residues within 4Å: Chain A: H.177, F.178, D.182, Y.185, D.186 Ligand excluded by PLIP UNX.25: 2 residues within 4Å: Chain A: L.209, V.218 Ligand excluded by PLIP UNX.26: 4 residues within 4Å: Chain A: D.258, R.260, W.285, Y.289 Ligand excluded by PLIP UNX.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.28: 1 residues within 4Å: Chain B: D.296 Ligand excluded by PLIP UNX.29: 3 residues within 4Å: Chain B: Y.32, N.33, K.34 Ligand excluded by PLIP UNX.30: 1 residues within 4Å: Chain B: D.88 Ligand excluded by PLIP UNX.31: 1 residues within 4Å: Chain B: G.107 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

James, L.I. et al., Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain. Nat. Chem. Biol. (2013)

Release Date

2012-06-27

Peptides

Lethal(3)malignant brain tumor-like protein 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lethal(3)malignant brain tumor-like protein 3