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

Crystal structure of L-proline dehydrogenase from P.horikoshii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.86 Å

Oligo State

hetero-4-4-mer

Ligands

4 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) FE.8: 5 residues within 4Å: Chain C: G.447, F.448, C.449, Q.450, G.451 No protein-ligand interaction detected (PLIP) FE.15: 5 residues within 4Å: Chain E: G.447, F.448, C.449, Q.450, G.451 No protein-ligand interaction detected (PLIP) FE.22: 5 residues within 4Å: Chain G: G.447, F.448, C.449, Q.450, G.451 No protein-ligand interaction detected (PLIP)

4 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 B, 3 interactions with chain A Hydrogen bonds: B:Y.169, A:T.433, A:T.433, A:D.434 Water bridges: B:E.168, B:E.168 SO4.9: 6 residues within 4Å: Chain C: G.431, I.432, T.433, D.434, I.437 Chain D: Y.169 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Y.169, C:T.433, C:T.433, C:D.434 Water bridges: D:E.168, D:E.168 SO4.16: 6 residues within 4Å: Chain E: G.431, I.432, T.433, D.434, I.437 Chain F: Y.169 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain E Water bridges: F:E.168, F:E.168 Hydrogen bonds: E:T.433, E:T.433, E:D.434, E:D.434 SO4.23: 6 residues within 4Å: Chain G: G.431, I.432, T.433, D.434, I.437 Chain H: Y.169 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:T.433, G:T.433, G:D.434, G:D.434 Water bridges: H:E.168, H:E.168

4 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: 9 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.261, B:W.304 Hydrogen bonds: B:F.45, B:R.302, A:Q.436, A:K.439, A:R.440, A:M.446, A:Q.450 Water bridges: B:R.46, B:T.275, B:R.302, A:K.439 Salt bridges: B:R.46, B:R.302, A:R.479 FMN.10: 16 residues within 4Å: Chain C: Q.436, K.439, R.440, H.443, M.446, Q.450, V.477, R.479 Chain D: F.45, R.46, C.47, D.147, I.229, I.261, R.302, W.304 16 PLIP interactions: 7 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:Q.436, C:K.439, C:R.440, C:M.446, C:Q.450, D:F.45, D:R.302 Water bridges: C:K.439, D:R.46, D:T.275, D:R.302 Salt bridges: C:R.479, D:R.46, D:R.302 Hydrophobic interactions: D:I.261, D:W.304 FMN.17: 16 residues within 4Å: Chain E: Q.436, K.439, R.440, H.443, M.446, Q.450, V.477, R.479 Chain F: F.45, R.46, C.47, D.147, I.229, I.261, R.302, W.304 18 PLIP interactions: 10 interactions with chain F, 8 interactions with chain E Hydrophobic interactions: F:I.261, F:W.304 Hydrogen bonds: F:F.45, F:R.302, E:Q.436, E:K.439, E:R.440, E:M.446, E:Q.450 Water bridges: F:T.255, F:T.255, F:T.275, F:R.302, E:K.439, E:R.479 Salt bridges: F:R.46, F:R.302, E:R.479 FMN.24: 16 residues within 4Å: Chain G: Q.436, K.439, R.440, H.443, M.446, Q.450, V.477, R.479 Chain H: F.45, R.46, C.47, D.147, I.229, I.261, R.302, W.304 18 PLIP interactions: 10 interactions with chain H, 8 interactions with chain G Hydrophobic interactions: H:I.261, H:W.304 Hydrogen bonds: H:F.45, H:R.302, G:Q.436, G:K.439, G:R.440, G:M.446, G:Q.450 Water bridges: H:T.255, H:T.255, H:T.275, H:R.302, G:K.439, G:R.479 Salt bridges: H:R.46, H:R.302, G:R.479

4 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 ATP.11: 25 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:G.116, C:G.117, C:G.117, C:A.119, C:E.138, C:E.138, C:R.139, C:R.139, C:D.145, C:M.146, C:A.183, C:A.183, C:A.217, C:S.351, C:S.351, C:S.351, C:N.361 Water bridges: C:G.120, C:A.352, C:A.352, C:R.452 Salt bridges: C:R.311, C:R.311, C:H.358 ATP.18: 25 residues within 4Å: Chain E: 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 23 PLIP interactions: 23 interactions with chain E Hydrogen bonds: E:G.116, E:G.117, E:G.117, E:A.119, E:E.138, E:R.139, E:R.139, E:D.145, E:M.146, E:A.183, E:A.183, E:A.217, E:S.351, E:S.351, E:S.351, E:N.361 Water bridges: E:G.120, E:A.352, E:A.352, E:R.452 Salt bridges: E:R.311, E:R.311, E:H.358 ATP.25: 25 residues within 4Å: Chain G: 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 23 PLIP interactions: 23 interactions with chain G Hydrogen bonds: G:G.116, G:G.117, G:G.117, G:A.119, G:E.138, G:R.139, G:R.139, G:D.145, G:M.146, G:A.183, G:A.183, G:A.217, G:S.351, G:S.351, G:S.351, G:N.361 Water bridges: G:G.120, G:A.352, G:A.352, G:R.452 Salt bridges: G:R.311, G:R.311, G:H.358

4 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 CXS.12: 6 residues within 4Å: Chain C: K.11, G.140, W.141, V.244, W.245, E.246 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.11, C:W.245 CXS.19: 6 residues within 4Å: Chain E: K.11, G.140, W.141, V.244, W.245, E.246 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:K.11, E:W.245 CXS.26: 6 residues within 4Å: Chain G: K.11, G.140, W.141, V.244, W.245, E.246 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:K.11, G:W.245

4 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 CL.13: 7 residues within 4Å: Chain D: N.202, Y.308, A.309, F.333, S.334, G.335 Ligands: FAD.14 Ligand excluded by PLIP CL.20: 7 residues within 4Å: Chain F: N.202, Y.308, A.309, F.333, S.334, G.335 Ligands: FAD.21 Ligand excluded by PLIP CL.27: 7 residues within 4Å: Chain H: N.202, Y.308, A.309, F.333, S.334, G.335 Ligands: FAD.28 Ligand excluded by PLIP

4 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 FAD.14: 36 residues within 4Å: Chain D: 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.13 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:Y.308 Hydrogen bonds: D:G.12, D:G.14, D:G.14, D:V.16, D:G.17, D:K.36, D:S.41, D:S.41, D:S.43, D:T.44, D:T.44, D:G.48, D:G.50, D:V.172, D:V.172, D:N.202, D:G.337, D:F.338, D:M.339 Water bridges: D:Y.87, D:A.203, D:A.203 pi-Cation interactions: D:K.36 FAD.21: 36 residues within 4Å: Chain F: 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.20 23 PLIP interactions: 23 interactions with chain F Hydrophobic interactions: F:Y.308 Hydrogen bonds: F:G.12, F:G.14, F:G.14, F:V.16, F:G.17, F:K.36, F:S.41, F:S.41, F:S.43, F:T.44, F:T.44, F:G.48, F:G.50, F:V.172, F:V.172, F:N.202, F:G.337, F:F.338, F:M.339 Water bridges: F:A.203, F:A.203 pi-Cation interactions: F:K.36 FAD.28: 36 residues within 4Å: Chain H: 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.27 23 PLIP interactions: 23 interactions with chain H Hydrophobic interactions: H:Y.308 Hydrogen bonds: H:G.12, H:G.14, H:G.14, H:V.16, H:G.17, H:K.36, H:S.41, H:S.41, H:S.43, H:T.44, H:T.44, H:G.48, H:G.50, H:V.172, H:V.172, H:N.202, H:G.337, H:F.338, H:M.339 Water bridges: H:A.203, H:A.203 pi-Cation interactions: H: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: ACEG
sarcosine oxidase: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
B

D
B

F
B

H
B

hypothetical protein PH1363

sarcosine oxidase

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