SMTL ID : 6byb.1

Crystal structure of L3MBTL1 MBT Domain with MBK14970

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

1 x EC7: (S)-N-(cyclopropylmethyl)-N~2~-methyl-N-[2-methyl-2-(1-methylpiperidin-4-yl)propyl]alaninamide(Non-covalent)

EC7.1: 7 residues within 4Å: Chain A: D.156, N.159, L.162, C.164, F.180, W.183, Y.187 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.162, A:W.183, A:Y.187 Hydrogen bonds: A:Y.187 Water bridges: A:N.159 Salt bridges: A:D.156 pi-Cation interactions: A:W.183

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

EDO.2: 3 residues within 4Å: Chain A: P.238, T.239, W.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.239, A:W.240 Water bridges: A:V.237, A:T.239 EDO.3: 5 residues within 4Å: Chain A: D.260, R.262, R.268, W.287, Y.291 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.262, A:R.268 Water bridges: A:D.260, A:R.262 EDO.4: 6 residues within 4Å: Chain A: K.151, S.167, T.169, H.179, D.181, N.182 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.167, A:S.167, A:N.182 Water bridges: A:H.179, A:F.180 EDO.5: 8 residues within 4Å: Chain A: V.23, A.31, T.33, P.304, A.305, G.306, W.307, K.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.31, A:A.305 Water bridges: A:K.310, A:K.310 EDO.6: 9 residues within 4Å: Chain A: L.25, F.26, Q.27, Q.30, H.248, F.250, A.297, D.298 Ligands: UNX.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.25, A:Q.27 EDO.7: 7 residues within 4Å: Chain A: Y.56, P.89, D.90, H.92, V.172, R.175, W.190 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.90, A:H.92, A:R.175, A:R.175 EDO.8: 5 residues within 4Å: Chain A: K.44, T.60, H.72, D.74, G.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.60, A:G.75 EDO.9: 2 residues within 4Å: Chain A: R.261, F.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.261 Water bridges: A:Y.291, A:Y.291

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

UNX.10: 2 residues within 4Å: Chain A: I.19, N.253 No protein-ligand interaction detected (PLIP) UNX.11: 3 residues within 4Å: Chain A: W.7, S.8, S.11 No protein-ligand interaction detected (PLIP) UNX.12: 3 residues within 4Å: Chain A: I.198, F.242, V.244 No protein-ligand interaction detected (PLIP) UNX.13: 1 residues within 4Å: Chain A: W.287 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Chain A: S.8, W.9 No protein-ligand interaction detected (PLIP) UNX.15: 2 residues within 4Å: Chain A: T.169, D.170 No protein-ligand interaction detected (PLIP) UNX.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.17: 2 residues within 4Å: Chain A: P.89, D.90 No protein-ligand interaction detected (PLIP) UNX.18: 5 residues within 4Å: Chain A: R.245, H.278, A.297, D.298 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) UNX.19: 1 residues within 4Å: Chain A: A.305 No protein-ligand interaction detected (PLIP) UNX.20: 3 residues within 4Å: Chain A: S.116, W.117, S.118 No protein-ligand interaction detected (PLIP) UNX.21: 3 residues within 4Å: Chain A: P.200, W.203, K.206 No protein-ligand interaction detected (PLIP) UNX.22: 4 residues within 4Å: Chain A: S.24, L.25, F.26, Q.27 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

DOBROVETSKY, E. et al., Crystal structure of L3MBTL1 MBT Domain with MBK14970. to be published

Release Date

2018-01-24

Peptides

Lethal(3)malignant brain tumor-like protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lethal(3)malignant brain tumor-like protein 1

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