SMTL ID : 2hba.4 (3 other biounits)

Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9) K12M

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-tetramer

Ligands

16 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 3 residues within 4Å: Chain A: M.1, D.23 Ligands: CL.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.23 ZN.2: 3 residues within 4Å: Chain A: D.8 Chain B: K.10 Ligands: CL.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.8, A:D.8, H2O.1 ZN.3: 3 residues within 4Å: Chain A: E.17 Ligands: CL.6, CL.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.17, A:E.17 ZN.4: 3 residues within 4Å: Ligands: CL.9, CL.10, IMD.12 No protein-ligand interaction detected (PLIP) ZN.5: 1 residues within 4Å: Ligands: ZN.17 No protein-ligand interaction detected (PLIP) ZN.13: 3 residues within 4Å: Chain B: M.1, D.23 Ligands: CL.23 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.23 ZN.14: 3 residues within 4Å: Chain A: K.10 Chain B: D.8 Ligands: CL.20 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.8, B:D.8, H2O.3 ZN.15: 3 residues within 4Å: Chain B: E.17 Ligands: CL.18, CL.19 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.17, B:E.17 ZN.16: 3 residues within 4Å: Ligands: CL.21, CL.22, IMD.24 No protein-ligand interaction detected (PLIP) ZN.17: 1 residues within 4Å: Ligands: ZN.5 No protein-ligand interaction detected (PLIP) ZN.25: 3 residues within 4Å: Chain C: M.1, D.23 Ligands: CL.28 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.23, H2O.4 ZN.26: 4 residues within 4Å: Chain C: D.8 Chain D: K.10 Ligands: CL.29, CL.30 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.8, H2O.5 ZN.27: 1 residues within 4Å: Ligands: CL.31 No protein-ligand interaction detected (PLIP) ZN.32: 3 residues within 4Å: Chain D: M.1, D.23 Ligands: CL.35 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.23, H2O.6 ZN.33: 4 residues within 4Å: Chain C: K.10 Chain D: D.8 Ligands: CL.36, CL.37 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.8, H2O.7 ZN.34: 1 residues within 4Å: Ligands: CL.38 No protein-ligand interaction detected (PLIP)

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

CL.6: 5 residues within 4Å: Chain A: E.17, K.19 Chain C: G.11 Ligands: ZN.3, CL.7 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: G.13, K.14, E.17, K.19 Ligands: ZN.3, CL.6 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: D.8 Chain B: K.10 Chain D: K.14 Ligands: ZN.2 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: A.22, Y.25 Ligands: ZN.4, CL.10, IMD.12 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Ligands: ZN.4, CL.9, IMD.12 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: M.1, D.23 Ligands: ZN.1 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain B: E.17, K.19 Chain D: G.11 Ligands: ZN.15, CL.19 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain B: G.13, K.14, E.17, K.19 Ligands: ZN.15, CL.18 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: K.10 Chain B: D.8 Chain C: K.14 Ligands: ZN.14 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain B: A.22, Y.25 Ligands: ZN.16, CL.22, IMD.24 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Ligands: ZN.16, CL.21, IMD.24 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain B: M.1, D.23 Ligands: ZN.13 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain C: M.1, V.21, D.23 Ligands: ZN.25 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain B: K.14 Chain C: D.8 Chain D: K.10 Ligands: ZN.26, CL.30 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain C: D.8 Ligands: ZN.26, CL.29 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain C: A.22, G.24, Y.25 Ligands: ZN.27 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain D: M.1, V.21, D.23 Ligands: ZN.32 Ligand excluded by PLIP CL.36: 5 residues within 4Å: Chain A: K.14 Chain C: K.10 Chain D: D.8 Ligands: ZN.33, CL.37 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain D: D.8 Ligands: ZN.33, CL.36 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain D: A.22, G.24, Y.25 Ligands: ZN.34 Ligand excluded by PLIP

2 x IMD: IMIDAZOLE(Non-functional Binders)

IMD.12: 3 residues within 4Å: Ligands: ZN.4, CL.9, CL.10 No protein-ligand interaction detected (PLIP) IMD.24: 3 residues within 4Å: Ligands: ZN.16, CL.21, CL.22 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cho, J.H. et al., Energetically significant networks of coupled interactions within an unfolded protein. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2007-05-29

Peptides

50S ribosomal protein L9: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
A

D
A

50S ribosomal protein L9

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