SMTL ID : 2ekg.1 (2 other biounits)

Structure of Thermus thermophilus Proline Dehydrogenase inactivated by N-propargylglycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 22 residues within 4Å: Chain A: K.119, D.153, M.154, V.181, Q.183, R.204, V.206, K.207, G.208, A.209, Y.210, A.245, T.246, H.247, D.248, P.249, Q.272, L.274, V.277, R.278, Y.295, R.313 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.245, A:Q.272, A:L.274 Hydrogen bonds: A:M.154, A:M.154, A:Q.183, A:R.204, A:K.207, A:G.208, A:G.208, A:A.209, A:H.247, A:D.248 Water bridges: A:R.278 Salt bridges: A:K.207, A:K.207, A:K.221 pi-Cation interactions: A:H.247 FAD.4: 20 residues within 4Å: Chain B: K.119, D.153, M.154, V.181, Q.183, R.204, V.206, K.207, G.208, A.209, Y.210, A.245, T.246, H.247, D.248, P.249, Q.272, L.274, V.277, Y.295 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.245, B:Q.272, B:L.274 Hydrogen bonds: B:M.154, B:M.154, B:Q.183, B:R.204, B:K.207, B:G.208, B:G.208, B:A.209, B:T.246, B:H.247, B:D.248 Water bridges: B:K.207, B:K.207, B:R.278 Salt bridges: B:K.207, B:K.207

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 8 residues within 4Å: Chain A: K.114, Y.115, F.149, R.151, N.202, Y.241, E.270, R.293 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.115 Hydrogen bonds: A:N.202 MPD.3: 4 residues within 4Å: Chain A: R.171, E.172, P.198, Y.199 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.172, A:P.198, A:Y.199 Water bridges: A:R.171 MPD.5: 8 residues within 4Å: Chain B: K.114, Y.115, F.149, R.151, N.202, Y.241, E.270, R.293 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.115, B:Y.115 Hydrogen bonds: B:N.202 MPD.6: 4 residues within 4Å: Chain B: R.171, E.172, P.198, Y.199 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

White, T.A. et al., Structural basis for the inactivation of Thermus thermophilus proline dehydrogenase by N-propargylglycine. Biochemistry (2008)

Release Date

2008-04-01

Peptides

Proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase

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