SMTL ID : 5d8h.1

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

11 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: G.16 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain A: A.33, G.53, U.54, C.57 No protein-ligand interaction detected (PLIP) MG.3: 6 residues within 4Å: Chain A: G.23, A.30, C.32, G.34, C.35 Ligands: NA.13 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: G.14 No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain A: G.31, A.58 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain A: U.25 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: G.7, G.70 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain A: G.73 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain C: K.111, M.114, L.115, S.116 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:K.111, C:M.114, C:S.116, H2O.3

4 x NA: SODIUM ION(Non-functional Binders)

NA.11: 2 residues within 4Å: Chain A: U.26, A.27 No protein-ligand interaction detected (PLIP) NA.12: 4 residues within 4Å: Chain A: G.18, G.19, U.20, U.21 No protein-ligand interaction detected (PLIP) NA.13: 5 residues within 4Å: Chain A: A.29, A.30, C.32, A.33 Ligands: MG.3 No protein-ligand interaction detected (PLIP) NA.16: 3 residues within 4Å: Chain B: D.26, M.28, R.81 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.26

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.14: 3 residues within 4Å: Chain A: G.16, A.17, C.60 No protein-ligand interaction detected (PLIP) TRS.15: 5 residues within 4Å: Chain A: A.17, G.18, U.20, G.47, G.49 No protein-ligand interaction detected (PLIP) TRS.17: 2 residues within 4Å: Chain B: E.74, N.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabdulkhakov, A.G. et al., CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON. To Be Published

Release Date

2016-08-24

Peptides

50S ribosomal protein L10: B
50S ribosomal protein L11: C
THIOSTREPTON: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

C
C

D
D

50S ribosomal protein L10

50S ribosomal protein L11

THIOSTREPTON

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