SMTL ID : 5ur2.3 (3 other biounits)

Crystal structure of proline utilization A (PutA) from Bdellovibrio bacteriovorus inactivated by N-propargylglycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-tetramer

Ligands

4 x P5F: N-propargylglycine-modified flavin adenine dinucleotide(Covalent)

P5F.1: 30 residues within 4Å: Chain A: K.198, D.239, M.240, V.271, Q.273, Y.275, R.300, V.302, K.303, G.304, A.305, Y.306, W.307, Y.324, T.325, N.326, K.327, S.330, A.353, S.354, H.355, N.356, Q.380, M.381, L.382, Y.403, E.422, E.427, S.428, W.429 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:K.198, A:D.239, A:A.353, A:Q.380, A:L.382, A:Y.403, A:Y.403, A:Y.403 Hydrogen bonds: A:M.240, A:M.240, A:Q.273, A:K.303, A:G.304, A:G.304, A:G.304, A:A.305, A:T.325, A:S.330, A:D.331, A:H.355, A:N.356, A:E.422, A:W.429 Water bridges: A:K.327, A:A.353, A:S.425 Salt bridges: A:K.303, A:K.303, A:K.327, A:H.355 pi-Stacking: A:W.307, A:W.307 P5F.2: 31 residues within 4Å: Chain B: K.198, D.239, M.240, V.271, Q.273, Y.275, R.300, V.302, K.303, G.304, A.305, Y.306, W.307, Y.324, T.325, N.326, K.327, S.330, D.331, A.353, S.354, H.355, N.356, Q.380, M.381, L.382, Y.403, E.422, E.427, S.428, W.429 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:K.198, B:D.239, B:A.353, B:Q.380, B:L.382, B:Y.403, B:Y.403 Hydrogen bonds: B:M.240, B:M.240, B:Q.273, B:K.303, B:G.304, B:G.304, B:G.304, B:A.305, B:T.325, B:S.330, B:D.331, B:H.355, B:N.356, B:E.422, B:W.429 Water bridges: B:K.327, B:A.353 Salt bridges: B:K.303, B:K.303, B:K.327 pi-Stacking: B:W.307, B:W.307 P5F.3: 30 residues within 4Å: Chain C: K.198, D.239, M.240, V.271, Q.273, Y.275, R.300, V.302, K.303, G.304, A.305, Y.306, W.307, Y.324, T.325, N.326, K.327, S.330, A.353, S.354, H.355, N.356, Q.380, M.381, L.382, Y.403, E.422, E.427, S.428, W.429 33 PLIP interactions: 33 interactions with chain C Hydrophobic interactions: C:K.198, C:D.239, C:A.353, C:Q.380, C:L.382, C:Y.403, C:Y.403, C:Y.403 Hydrogen bonds: C:M.240, C:M.240, C:Q.273, C:K.303, C:G.304, C:G.304, C:G.304, C:A.305, C:T.325, C:S.330, C:D.331, C:H.355, C:H.355, C:N.356, C:E.422, C:W.429 Water bridges: C:K.327, C:A.353, C:S.425 Salt bridges: C:K.303, C:K.303, C:K.327, C:H.355 pi-Stacking: C:W.307, C:W.307 P5F.4: 31 residues within 4Å: Chain D: K.198, D.239, M.240, V.271, Q.273, Y.275, R.300, V.302, K.303, G.304, A.305, Y.306, W.307, Y.324, T.325, N.326, K.327, S.330, D.331, A.353, S.354, H.355, N.356, Q.380, M.381, L.382, Y.403, E.422, E.427, S.428, W.429 30 PLIP interactions: 30 interactions with chain D Hydrophobic interactions: D:K.198, D:D.239, D:A.353, D:Q.380, D:L.382, D:Y.403, D:Y.403 Hydrogen bonds: D:M.240, D:M.240, D:Q.273, D:K.303, D:G.304, D:G.304, D:G.304, D:A.305, D:T.325, D:S.330, D:D.331, D:H.355, D:H.355, D:N.356, D:E.422, D:W.429 Water bridges: D:K.327, D:A.353 Salt bridges: D:K.303, D:K.303, D:K.327 pi-Stacking: D:W.307, D:W.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korasick, D.A. et al., Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure. FEBS J. (2017)

Release Date

2017-08-02

Peptides

Bifunctional protein PutA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Bifunctional protein PutA

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