SMTL ID : 1y56.2 (3 other biounits)

Crystal structure of L-proline dehydrogenase from P.horikoshii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.86 Å

Oligo State

hetero-1-1-mer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: G.447, F.448, C.449, Q.450, G.451 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: G.431, I.432, T.433, D.434, I.437 Chain B: Y.169 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.433, A:T.433, A:D.434, B:Y.169 Water bridges: B:E.168, B:E.168

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 16 residues within 4Å: Chain A: Q.436, K.439, R.440, H.443, M.446, Q.450, V.477, R.479 Chain B: F.45, R.46, C.47, D.147, I.229, I.261, R.302, W.304 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:Q.436, A:K.439, A:R.440, A:M.446, A:Q.450, B:F.45, B:R.302 Water bridges: A:K.439, B:R.46, B:T.275, B:R.302 Salt bridges: A:R.479, B:R.46, B:R.302 Hydrophobic interactions: B:I.261, B:W.304

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 25 residues within 4Å: Chain A: I.114, G.115, G.116, G.117, P.118, A.119, E.137, E.138, R.139, G.144, D.145, T.181, S.182, A.183, A.214, T.215, G.216, A.217, R.311, G.350, S.351, H.358, N.361, I.482, K.483 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.116, A:G.117, A:G.117, A:A.119, A:E.138, A:E.138, A:R.139, A:R.139, A:D.145, A:M.146, A:A.183, A:A.183, A:A.217, A:S.351, A:S.351, A:S.351, A:N.361 Water bridges: A:G.120, A:A.352, A:A.352, A:R.452 Salt bridges: A:R.311, A:R.311, A:H.358

1 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.5: 6 residues within 4Å: Chain A: K.11, G.140, W.141, V.244, W.245, E.246 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.11, A:W.245

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 7 residues within 4Å: Chain B: N.202, Y.308, A.309, F.333, S.334, G.335 Ligands: FAD.7 Ligand excluded by PLIP

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.7: 36 residues within 4Å: Chain B: I.11, G.12, G.14, I.15, V.16, G.17, I.34, E.35, K.36, S.41, S.43, T.44, R.46, C.47, G.48, T.49, G.50, T.170, E.171, V.172, A.200, T.201, N.202, W.204, I.208, Y.251, G.306, Y.307, Y.308, F.333, G.335, H.336, G.337, F.338, M.339 Ligands: CL.6 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:Y.308 Hydrogen bonds: B:G.12, B:G.14, B:G.14, B:V.16, B:G.17, B:K.36, B:S.41, B:S.41, B:S.43, B:T.44, B:T.44, B:G.48, B:G.50, B:V.172, B:V.172, B:N.202, B:G.337, B:F.338, B:M.339 Water bridges: B:Y.87, B:A.203, B:A.203 pi-Cation interactions: B:K.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsuge, H. et al., Crystal structure of a novel FAD-, FMN-, and ATP-containing L-proline dehydrogenase complex from Pyrococcus horikoshii. J.Biol.Chem. (2005)

Release Date

2005-07-26

Peptides

hypothetical protein PH1363: A
sarcosine oxidase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

hypothetical protein PH1363

sarcosine oxidase

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