SMTL ID : 4ckj.1

Crystal structure of RET tyrosine kinase domain bound to adenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x ADN: ADENOSINE(Non-covalent)

ADN.1: 11 residues within 4Å: Chain A: L.31, G.32, V.39, A.57, V.105, E.106, Y.107, A.108, S.112, L.182 Ligands: FMT.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.106, A:A.108, A:S.112, A:D.193 Water bridges: A:S.112, A:S.112, A:S.112 ADN.18: 11 residues within 4Å: Chain B: L.31, G.32, V.39, A.57, V.105, E.106, Y.107, A.108, S.112, L.182 Ligands: FMT.20 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.106, B:A.108, B:S.112, B:D.193 Water bridges: B:S.112, B:S.112, B:S.112

32 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 5 residues within 4Å: Chain A: K.29, L.31, K.41, Y.107 Ligands: FMT.3 Ligand excluded by PLIP FMT.3: 7 residues within 4Å: Chain A: L.31, Y.107, A.108, K.109, G.111 Ligands: ADN.1, FMT.2 Ligand excluded by PLIP FMT.4: 3 residues within 4Å: Chain A: K.23, N.24, H.46 Ligand excluded by PLIP FMT.5: 3 residues within 4Å: Chain A: K.38, K.62, E.63 Ligand excluded by PLIP FMT.6: 9 residues within 4Å: Chain A: G.1, P.2, L.3, S.4 Chain B: Q.211, L.224, F.225, H.227, F.262 Ligand excluded by PLIP FMT.7: 5 residues within 4Å: Chain A: R.71, K.208, R.213 Chain B: S.210, Q.211 Ligand excluded by PLIP FMT.8: 5 residues within 4Å: Chain A: R.118, T.247, L.248, G.249, G.250 Ligand excluded by PLIP FMT.9: 6 residues within 4Å: Chain A: R.174, L.196, K.208, G.212, R.213, I.214 Ligand excluded by PLIP FMT.10: 2 residues within 4Å: Chain A: R.209 Chain B: R.209 Ligand excluded by PLIP FMT.11: 9 residues within 4Å: Chain A: K.208, S.210, Q.211, G.212, M.219, S.223, H.227, Y.229 Chain B: P.67 Ligand excluded by PLIP FMT.12: 5 residues within 4Å: Chain A: F.225, F.262, K.266 Chain B: S.4, D.8 Ligand excluded by PLIP FMT.13: 3 residues within 4Å: Chain A: D.204, T.230, T.231 Ligand excluded by PLIP FMT.14: 3 residues within 4Å: Chain A: R.71, L.74, S.75 Ligand excluded by PLIP FMT.15: 4 residues within 4Å: Chain A: K.109, Y.110, E.185, G.186 Ligand excluded by PLIP FMT.16: 3 residues within 4Å: Chain A: H.85, H.87, Q.161 Ligand excluded by PLIP FMT.17: 6 residues within 4Å: Chain A: L.80, V.83, V.88, I.89, K.90, L.91 Ligand excluded by PLIP FMT.19: 5 residues within 4Å: Chain B: K.29, L.31, K.41, Y.107 Ligands: FMT.20 Ligand excluded by PLIP FMT.20: 7 residues within 4Å: Chain B: L.31, Y.107, A.108, K.109, G.111 Ligands: ADN.18, FMT.19 Ligand excluded by PLIP FMT.21: 3 residues within 4Å: Chain B: K.23, N.24, H.46 Ligand excluded by PLIP FMT.22: 3 residues within 4Å: Chain B: K.38, K.62, E.63 Ligand excluded by PLIP FMT.23: 9 residues within 4Å: Chain A: Q.211, L.224, F.225, H.227, F.262 Chain B: G.1, P.2, L.3, S.4 Ligand excluded by PLIP FMT.24: 5 residues within 4Å: Chain A: S.210, Q.211 Chain B: R.71, K.208, R.213 Ligand excluded by PLIP FMT.25: 5 residues within 4Å: Chain B: R.118, T.247, L.248, G.249, G.250 Ligand excluded by PLIP FMT.26: 6 residues within 4Å: Chain B: R.174, L.196, K.208, G.212, R.213, I.214 Ligand excluded by PLIP FMT.27: 2 residues within 4Å: Chain A: R.209 Chain B: R.209 Ligand excluded by PLIP FMT.28: 9 residues within 4Å: Chain A: P.67 Chain B: K.208, S.210, Q.211, G.212, M.219, S.223, H.227, Y.229 Ligand excluded by PLIP FMT.29: 5 residues within 4Å: Chain A: S.4, D.8 Chain B: F.225, F.262, K.266 Ligand excluded by PLIP FMT.30: 3 residues within 4Å: Chain B: D.204, T.230, T.231 Ligand excluded by PLIP FMT.31: 3 residues within 4Å: Chain B: R.71, L.74, S.75 Ligand excluded by PLIP FMT.32: 4 residues within 4Å: Chain B: K.109, Y.110, E.185, G.186 Ligand excluded by PLIP FMT.33: 3 residues within 4Å: Chain B: H.85, H.87, Q.161 Ligand excluded by PLIP FMT.34: 6 residues within 4Å: Chain B: L.80, V.83, V.88, I.89, K.90, L.91 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plaza-Menacho, I. et al., Oncogenic RET kinase domain mutations perturb the autophosphorylation trajectory by enhancing substrate presentation in trans. Mol. Cell (2014)

Release Date

2014-03-05

Peptides

PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET

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