SMTL ID : 2x2u.1

First two Cadherin-like domains from Human RET

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: H.75, W.78, E.79, S.82, F.121, N.123 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 6 residues within 4Å: Chain B: H.75, W.78, E.79, S.82, F.121, N.123 No protein-ligand interaction detected (PLIP)

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

UNX.2: 14 residues within 4Å: Chain A: T.47, Y.48 Ligands: UNX.3, UNX.4, UNX.5, UNX.7, UNX.8, UNX.9, UNX.26, UNX.28, UNX.29, UNX.30, UNX.31, UNX.34 Ligand excluded by PLIP UNX.3: 8 residues within 4Å: Chain A: T.47, Y.48 Ligands: UNX.2, UNX.5, UNX.8, UNX.29, UNX.30, UNX.34 Ligand excluded by PLIP UNX.4: 18 residues within 4Å: Chain A: Y.94, Y.118 Ligands: UNX.2, UNX.5, UNX.6, UNX.7, UNX.9, UNX.10, UNX.11, UNX.24, UNX.26, UNX.27, UNX.28, UNX.29, UNX.30, UNX.31, UNX.32, UNX.33 Ligand excluded by PLIP UNX.5: 18 residues within 4Å: Chain A: G.46, Y.48, R.49, Y.94 Ligands: UNX.2, UNX.3, UNX.4, UNX.6, UNX.7, UNX.9, UNX.10, UNX.26, UNX.28, UNX.29, UNX.30, UNX.31, UNX.32, UNX.33 Ligand excluded by PLIP UNX.6: 16 residues within 4Å: Chain A: Y.118 Chain B: R.49 Ligands: UNX.4, UNX.5, UNX.7, UNX.9, UNX.10, UNX.24, UNX.26, UNX.27, UNX.28, UNX.29, UNX.30, UNX.31, UNX.32, UNX.33 Ligand excluded by PLIP UNX.7: 19 residues within 4Å: Chain A: Y.118 Chain B: Y.48 Ligands: UNX.2, UNX.4, UNX.5, UNX.6, UNX.8, UNX.9, UNX.10, UNX.24, UNX.25, UNX.26, UNX.27, UNX.28, UNX.29, UNX.30, UNX.31, UNX.32, UNX.33 Ligand excluded by PLIP UNX.8: 13 residues within 4Å: Chain B: Y.118 Ligands: UNX.2, UNX.3, UNX.7, UNX.9, UNX.12, UNX.24, UNX.25, UNX.26, UNX.27, UNX.28, UNX.29, UNX.31 Ligand excluded by PLIP UNX.9: 18 residues within 4Å: Chain B: R.49 Ligands: UNX.2, UNX.4, UNX.5, UNX.6, UNX.7, UNX.8, UNX.10, UNX.11, UNX.24, UNX.26, UNX.27, UNX.28, UNX.29, UNX.30, UNX.31, UNX.32, UNX.33 Ligand excluded by PLIP UNX.10: 16 residues within 4Å: Chain A: R.49 Chain B: R.49, Y.118 Ligands: UNX.4, UNX.5, UNX.6, UNX.7, UNX.9, UNX.11, UNX.26, UNX.27, UNX.28, UNX.29, UNX.31, UNX.32, UNX.33 Ligand excluded by PLIP UNX.11: 12 residues within 4Å: Chain A: R.49 Chain B: Y.94, Y.118 Ligands: UNX.4, UNX.9, UNX.10, UNX.26, UNX.27, UNX.28, UNX.29, UNX.31, UNX.32 Ligand excluded by PLIP UNX.12: 5 residues within 4Å: Chain B: T.47, T.92 Ligands: UNX.8, UNX.24, UNX.25 Ligand excluded by PLIP UNX.24: 14 residues within 4Å: Chain B: T.47, Y.48 Ligands: UNX.4, UNX.6, UNX.7, UNX.8, UNX.9, UNX.12, UNX.25, UNX.26, UNX.27, UNX.29, UNX.30, UNX.31 Ligand excluded by PLIP UNX.25: 8 residues within 4Å: Chain B: T.47, Y.48 Ligands: UNX.7, UNX.8, UNX.12, UNX.24, UNX.27, UNX.30 Ligand excluded by PLIP UNX.26: 18 residues within 4Å: Chain B: Y.94, Y.118 Ligands: UNX.2, UNX.4, UNX.5, UNX.6, UNX.7, UNX.8, UNX.9, UNX.10, UNX.11, UNX.24, UNX.27, UNX.28, UNX.29, UNX.31, UNX.32, UNX.33 Ligand excluded by PLIP UNX.27: 18 residues within 4Å: Chain B: G.46, Y.48, R.49, Y.94 Ligands: UNX.4, UNX.6, UNX.7, UNX.8, UNX.9, UNX.10, UNX.11, UNX.24, UNX.25, UNX.26, UNX.28, UNX.29, UNX.31, UNX.32 Ligand excluded by PLIP UNX.28: 16 residues within 4Å: Chain A: R.49 Chain B: Y.118 Ligands: UNX.2, UNX.4, UNX.5, UNX.6, UNX.7, UNX.8, UNX.9, UNX.10, UNX.11, UNX.26, UNX.27, UNX.29, UNX.31, UNX.32 Ligand excluded by PLIP UNX.29: 19 residues within 4Å: Chain A: Y.48 Chain B: Y.118 Ligands: UNX.2, UNX.3, UNX.4, UNX.5, UNX.6, UNX.7, UNX.8, UNX.9, UNX.10, UNX.11, UNX.24, UNX.26, UNX.27, UNX.28, UNX.30, UNX.31, UNX.32 Ligand excluded by PLIP UNX.30: 13 residues within 4Å: Chain A: Y.118 Ligands: UNX.2, UNX.3, UNX.4, UNX.5, UNX.6, UNX.7, UNX.9, UNX.24, UNX.25, UNX.29, UNX.31, UNX.34 Ligand excluded by PLIP UNX.31: 18 residues within 4Å: Chain A: R.49 Ligands: UNX.2, UNX.4, UNX.5, UNX.6, UNX.7, UNX.8, UNX.9, UNX.10, UNX.11, UNX.24, UNX.26, UNX.27, UNX.28, UNX.29, UNX.30, UNX.32, UNX.33 Ligand excluded by PLIP UNX.32: 16 residues within 4Å: Chain A: R.49, Y.118 Chain B: R.49 Ligands: UNX.4, UNX.5, UNX.6, UNX.7, UNX.9, UNX.10, UNX.11, UNX.26, UNX.27, UNX.28, UNX.29, UNX.31, UNX.33 Ligand excluded by PLIP UNX.33: 12 residues within 4Å: Chain A: Y.94, Y.118 Chain B: R.49 Ligands: UNX.4, UNX.5, UNX.6, UNX.7, UNX.9, UNX.10, UNX.26, UNX.31, UNX.32 Ligand excluded by PLIP UNX.34: 5 residues within 4Å: Chain A: T.47, T.92 Ligands: UNX.2, UNX.3, UNX.30 Ligand excluded by PLIP

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

SO4.13: 2 residues within 4Å: Chain A: R.135, V.228 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain A: G.41, Q.42, H.43, Y.45, R.51, K.96 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain A: W.57, R.71, S.76, S.77, K.80 Ligand excluded by PLIP SO4.16: 7 residues within 4Å: Chain A: R.49, Y.94, K.96, E.108, C.109 Chain B: R.49, Q.110 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: R.206, E.207, K.208 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain A: Y.176, R.177, P.190 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: A.128, C.129, S.130 Ligand excluded by PLIP SO4.20: 6 residues within 4Å: Chain A: Y.24, H.26, T.156, H.158, Q.159, E.194 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain B: R.135, V.228 Ligand excluded by PLIP SO4.36: 6 residues within 4Å: Chain B: G.41, Q.42, H.43, Y.45, R.51, K.96 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain B: W.57, R.71, S.76, S.77, K.80 Ligand excluded by PLIP SO4.38: 7 residues within 4Å: Chain A: R.49, Q.110 Chain B: R.49, Y.94, K.96, E.108, C.109 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain B: R.206, E.207, K.208 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain B: Y.176, R.177, P.190 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain B: A.128, C.129, S.130 Ligand excluded by PLIP SO4.42: 6 residues within 4Å: Chain B: Y.24, H.26, T.156, H.158, Q.159, E.194 Ligand excluded by PLIP

4 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.21: 7 residues within 4Å: Chain A: K.11, Y.13, F.126, E.136, F.139, L.162 Ligands: BU1.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.11, A:E.136 Hydrogen bonds: A:F.139 Water bridges: A:K.11 BU1.22: 8 residues within 4Å: Chain A: W.9, E.10, K.11, S.120, P.140, E.141, L.162 Ligands: BU1.21 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.140, A:E.141 Hydrogen bonds: A:E.10, A:E.10 Water bridges: A:S.120, A:S.120 BU1.43: 7 residues within 4Å: Chain B: K.11, Y.13, F.126, E.136, F.139, L.162 Ligands: BU1.44 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.11, B:E.136 Hydrogen bonds: B:Y.13, B:F.139 Water bridges: B:K.11 BU1.44: 8 residues within 4Å: Chain B: W.9, E.10, K.11, S.120, P.140, E.141, L.162 Ligands: BU1.43 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.140, B:E.141 Hydrogen bonds: B:E.10, B:E.10 Water bridges: B:S.120, B:S.120

Links

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Citation

Kjaer, S. et al., Mammal-restricted elements predispose human RET to folding impairment by HSCR mutations. Nat. Struct. Mol. Biol. (2010)

Release Date

2010-05-19

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