SMTL ID : 4lr3.2 (3 other biounits)

Crystal structure of E. coli YfbU at 2.5 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: Q.14, M.17 Chain B: Q.14, M.17 Chain C: Q.14, M.17 Chain D: Q.14, M.17 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:Q.14, D:Q.14, A:Q.14, C:Q.14 PO4.2: 6 residues within 4Å: Chain A: Y.69, R.88, R.89, K.136, M.140, I.162 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.69 Water bridges: A:Y.69, A:T.91, A:T.91 Salt bridges: A:R.89, A:K.136 PO4.5: 6 residues within 4Å: Chain A: Q.7, I.10 Chain B: Q.7 Chain C: Q.7 Chain D: Q.7, I.10 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: D:Q.7, B:Q.7, A:Q.7, C:Q.7 Water bridges: D:T.4 PO4.6: 6 residues within 4Å: Chain B: Y.69, R.88, R.89, T.91, M.140, I.162 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.69, B:Y.69 Salt bridges: B:R.89 PO4.10: 6 residues within 4Å: Chain C: Y.69, R.89, M.133, K.136, M.140, I.162 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.69 Salt bridges: C:R.89, C:K.136

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

MG.3: 2 residues within 4Å: Chain A: E.114 Chain B: E.46 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: R.60 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: E.114 Chain C: E.46 No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain C: E.114 Chain D: E.46 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain D: D.64 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain A: E.46 Chain D: E.114 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.114, H2O.1, H2O.1, H2O.1, H2O.10 MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-04-30

Peptides

protein YfbU: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

protein YfbU

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