SMTL ID : 2hvf.2 (1 other biounit)

Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9), G34dA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: D.8 Ligands: CL.7, CL.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.8, H2O.2 ZN.2: 2 residues within 4Å: Chain A: D.23 Ligands: CL.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.23, A:D.23, H2O.1, H2O.1, H2O.2 ZN.3: 5 residues within 4Å: Chain A: Q.50 Chain B: Q.50 Ligands: IMD.9, ZN.13, IMD.19 No protein-ligand interaction detected (PLIP) ZN.4: 3 residues within 4Å: Chain A: E.17, K.19 Ligands: CL.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.17, A:E.17, H2O.3 ZN.11: 3 residues within 4Å: Chain B: D.8 Ligands: CL.17, CL.18 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.8, H2O.5 ZN.12: 2 residues within 4Å: Chain B: D.23 Ligands: CL.16 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.23, B:D.23, H2O.3, H2O.4, H2O.4 ZN.13: 5 residues within 4Å: Chain A: Q.50 Chain B: Q.50 Ligands: ZN.3, IMD.9, IMD.19 No protein-ligand interaction detected (PLIP) ZN.14: 3 residues within 4Å: Chain B: E.17, K.19 Ligands: CL.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.17, B:E.17, H2O.5

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

CL.5: 5 residues within 4Å: Chain A: G.13, K.14, E.17, K.19 Ligands: ZN.4 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: M.1, D.23 Ligands: ZN.2 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: D.8, K.14 Ligands: ZN.1, CL.8 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: D.8 Ligands: ZN.1, CL.7 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: G.13, K.14, E.17, K.19 Ligands: ZN.14 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: M.1, D.23 Ligands: ZN.12 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: D.8, K.14 Ligands: ZN.11, CL.18 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: D.8 Ligands: ZN.11, CL.17 Ligand excluded by PLIP

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.9: 9 residues within 4Å: Chain A: I.37, N.43, Q.50 Chain B: I.37, N.43, Q.50 Ligands: ZN.3, ZN.13, IMD.19 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.50, B:Q.50 Hydrogen bonds: A:Q.50 IMD.19: 9 residues within 4Å: Chain A: I.37, N.43, Q.50 Chain B: I.37, N.43, Q.50 Ligands: ZN.3, IMD.9, ZN.13 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.50, A:Q.50 Hydrogen bonds: B:Q.50

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.10: 1 residues within 4Å: Chain A: G.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.11 ACY.20: 1 residues within 4Å: Chain B: G.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anil, B. et al., Detecting and quantifying strain in protein folding. To be Published

Release Date

2007-06-12

Peptides

50S ribosomal protein L9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

50S ribosomal protein L9

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