SMTL ID : 3els.2 (1 other biounit)

Crystal Structure of Yeast Pml1p, Residues 51-204

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: D.82 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.82, H2O.1, H2O.1 MG.7: 1 residues within 4Å: Chain B: D.82 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.82, H2O.8, H2O.8 MG.13: 1 residues within 4Å: Chain C: D.82 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.82, H2O.15, H2O.15 MG.19: 1 residues within 4Å: Chain D: D.82 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.82, H2O.22, H2O.22 MG.25: 1 residues within 4Å: Chain E: D.82 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.82, H2O.29, H2O.29 MG.31: 1 residues within 4Å: Chain F: D.82 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.82, H2O.36, H2O.36

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.8, CL.14 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.2, CL.14 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.2, CL.8 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain D: R.130 Chain E: R.130 Chain F: R.130 Ligands: CL.26, CL.32 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain D: R.130 Chain E: R.130 Chain F: R.130 Ligands: CL.20, CL.32 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain D: R.130 Chain E: R.130 Chain F: R.130 Ligands: CL.20, CL.26 Ligand excluded by PLIP

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: M.31, Y.32, E.33, R.49, D.51, N.53, V.158 Chain D: Y.37, K.42, G.45 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: D.16, R.29, M.31, D.51, N.53 Chain D: D.43 Ligands: GOL.5 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: D.16, D.20, R.29 Ligands: GOL.4 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain D: K.39, N.123, V.139, T.141, E.146, E.152 Chain F: V.102, R.103 Ligand excluded by PLIP GOL.9: 10 residues within 4Å: Chain B: M.31, Y.32, E.33, R.49, D.51, N.53, V.158 Chain F: Y.37, K.42, G.45 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain B: D.16, R.29, M.31, D.51, N.53 Chain F: D.43 Ligands: GOL.11 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain B: D.16, D.20, R.29 Ligands: GOL.10 Ligand excluded by PLIP GOL.12: 8 residues within 4Å: Chain E: V.102, R.103 Chain F: K.39, N.123, V.139, T.141, E.146, E.152 Ligand excluded by PLIP GOL.15: 10 residues within 4Å: Chain C: M.31, Y.32, E.33, R.49, D.51, N.53, V.158 Chain E: Y.37, K.42, G.45 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain C: D.16, R.29, M.31, D.51, N.53 Chain E: D.43 Ligands: GOL.17 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain C: D.16, D.20, R.29 Ligands: GOL.16 Ligand excluded by PLIP GOL.18: 8 residues within 4Å: Chain D: V.102, R.103 Chain E: K.39, N.123, V.139, T.141, E.146, E.152 Ligand excluded by PLIP GOL.21: 10 residues within 4Å: Chain A: Y.37, K.42, G.45 Chain D: M.31, Y.32, E.33, R.49, D.51, N.53, V.158 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain A: D.43 Chain D: D.16, R.29, M.31, D.51, N.53 Ligands: GOL.23 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain D: D.16, D.20, R.29 Ligands: GOL.22 Ligand excluded by PLIP GOL.24: 8 residues within 4Å: Chain A: K.39, N.123, V.139, T.141, E.146, E.152 Chain C: V.102, R.103 Ligand excluded by PLIP GOL.27: 10 residues within 4Å: Chain C: Y.37, K.42, G.45 Chain E: M.31, Y.32, E.33, R.49, D.51, N.53, V.158 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain C: D.43 Chain E: D.16, R.29, M.31, D.51, N.53 Ligands: GOL.29 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain E: D.16, D.20, R.29 Ligands: GOL.28 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain B: V.102, R.103 Chain C: K.39, N.123, V.139, T.141, E.146, E.152 Ligand excluded by PLIP GOL.33: 10 residues within 4Å: Chain B: Y.37, K.42, G.45 Chain F: M.31, Y.32, E.33, R.49, D.51, N.53, V.158 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain B: D.43 Chain F: D.16, R.29, M.31, D.51, N.53 Ligands: GOL.35 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain F: D.16, D.20, R.29 Ligands: GOL.34 Ligand excluded by PLIP GOL.36: 8 residues within 4Å: Chain A: V.102, R.103 Chain B: K.39, N.123, V.139, T.141, E.146, E.152 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trowitzsch, S. et al., Crystal structure of the Pml1p subunit of the yeast precursor mRNA retention and splicing complex. J.Mol.Biol. (2009)

Release Date

2009-02-10

Peptides

Pre-mRNA leakage protein 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Pre-mRNA leakage protein 1

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