SMTL ID : 5v85.1

The crystal structure of the protein of DegV family COG1307 from Ruminococcus gnavus ATCC 29149 (alternative refinement of PDB 3JR7 with Vaccenic acid)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x VCA: VACCENIC ACID(Non-covalent)

VCA.1: 19 residues within 4Å: Chain A: L.47, T.80, S.81, C.82, L.108, S.109, G.110, R.137, S.138, A.139, T.176, F.178, R.191, S.211, G.215, T.216, S.285, Y.288, I.295 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.47, A:A.139, A:T.176, A:F.178, A:F.178, A:Y.288, A:Y.288, A:Y.288, A:I.295 Hydrogen bonds: A:T.80, A:G.110 Water bridges: A:R.191, A:R.191 Salt bridges: A:R.191 VCA.6: 19 residues within 4Å: Chain B: L.47, T.80, S.81, C.82, L.108, S.109, G.110, R.137, S.138, A.139, T.176, F.178, R.191, S.211, G.215, T.216, S.285, Y.288, I.295 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.47, B:A.139, B:T.176, B:F.178, B:F.178, B:Y.288, B:Y.288, B:Y.288, B:I.295 Hydrogen bonds: B:T.80, B:T.80, B:G.110 Water bridges: B:R.191, B:R.191 Salt bridges: B:R.191

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

PO4.2: 5 residues within 4Å: Chain A: A.223, R.224, K.228, K.232 Ligands: PO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.224 Water bridges: A:K.232 Salt bridges: A:K.232 PO4.3: 4 residues within 4Å: Chain A: I.205, K.222, R.224 Ligands: PO4.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.224 Salt bridges: A:R.224 PO4.4: 3 residues within 4Å: Chain A: Q.130, T.159, F.160 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.130, A:Q.130, A:F.160 Water bridges: A:R.98, A:E.161 PO4.7: 4 residues within 4Å: Chain B: K.23, C.94, D.95, A.96 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.95, B:D.95, B:A.96 Salt bridges: B:K.23

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

NA.5: 1 residues within 4Å: Chain A: R.87 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.84, A:S.84 NA.8: 1 residues within 4Å: Chain B: C.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cuypers, M.G. et al., The crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein loaded with palmitic acid to 1.83 Angstroem resolution. J.Biol.Chem. (2018)

Release Date

2018-11-21

Peptides

EDD domain protein, DegV family: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

EDD domain protein, DegV family

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