SMTL ID : 2bjk.1

Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from Thermus with bound NAD and citrate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-hexamer

Ligands

6 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 28 residues within 4Å: Chain A: I.180, A.181, P.182, W.183, N.184, I.189, K.207, P.208, A.209, E.210, G.240, E.241, G.244, A.245, F.258, T.259, G.260, S.261, V.264, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485 Ligands: FLC.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.189, A:T.259 Hydrogen bonds: A:A.181, A:A.181, A:W.183, A:K.207, A:E.210, A:G.240, A:S.261, A:T.289, A:E.417 Water bridges: A:W.183, A:E.241, A:S.261, A:L.262, A:E.417, A:E.417 NAD.8: 28 residues within 4Å: Chain B: I.180, A.181, P.182, W.183, N.184, I.189, K.207, P.208, A.209, E.210, G.240, E.241, G.244, A.245, F.258, T.259, G.260, S.261, V.264, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485 Ligands: FLC.9 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.189, B:T.259 Hydrogen bonds: B:A.181, B:A.181, B:W.183, B:K.207, B:E.210, B:G.240, B:S.261, B:T.289, B:E.417 Water bridges: B:W.183, B:S.261, B:L.262, B:K.267, B:E.288, B:E.288, B:E.417 NAD.16: 28 residues within 4Å: Chain C: I.180, A.181, P.182, W.183, N.184, I.189, K.207, P.208, A.209, E.210, G.240, E.241, G.244, A.245, F.258, T.259, G.260, S.261, V.264, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485 Ligands: FLC.17 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:I.189, C:T.259 Hydrogen bonds: C:A.181, C:A.181, C:W.183, C:K.207, C:E.210, C:G.240, C:S.261, C:T.289, C:E.417 Water bridges: C:W.183, C:E.241, C:S.261, C:L.262, C:E.417, C:E.417 NAD.23: 28 residues within 4Å: Chain D: I.180, A.181, P.182, W.183, N.184, I.189, K.207, P.208, A.209, E.210, G.240, E.241, G.244, A.245, F.258, T.259, G.260, S.261, V.264, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485 Ligands: FLC.24 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.189, D:T.259 Hydrogen bonds: D:A.181, D:A.181, D:W.183, D:K.207, D:E.210, D:G.240, D:S.261, D:T.289, D:E.417 Water bridges: D:W.183, D:S.261, D:L.262, D:K.267, D:E.288, D:E.288, D:E.417 NAD.31: 28 residues within 4Å: Chain E: I.180, A.181, P.182, W.183, N.184, I.189, K.207, P.208, A.209, E.210, G.240, E.241, G.244, A.245, F.258, T.259, G.260, S.261, V.264, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485 Ligands: FLC.32 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:I.189, E:T.259 Hydrogen bonds: E:A.181, E:A.181, E:W.183, E:K.207, E:E.210, E:G.240, E:S.261, E:T.289, E:E.417 Water bridges: E:W.183, E:E.241, E:S.261, E:L.262, E:E.417, E:E.417 NAD.38: 28 residues within 4Å: Chain F: I.180, A.181, P.182, W.183, N.184, I.189, K.207, P.208, A.209, E.210, G.240, E.241, G.244, A.245, F.258, T.259, G.260, S.261, V.264, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485 Ligands: FLC.39 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:I.189, F:T.259 Hydrogen bonds: F:A.181, F:A.181, F:W.183, F:K.207, F:E.210, F:G.240, F:S.261, F:T.289, F:E.417 Water bridges: F:W.183, F:S.261, F:L.262, F:K.267, F:E.288, F:E.288, F:E.417

6 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 11 residues within 4Å: Chain A: E.137, N.184, F.185, K.321, C.322, S.323, T.476, G.477, A.478, F.485 Ligands: NAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.185, A:F.185 Hydrogen bonds: A:N.184, A:C.322, A:S.323, A:S.323, A:S.323, A:G.477, A:A.478 Water bridges: A:E.137 FLC.9: 11 residues within 4Å: Chain B: E.137, N.184, F.185, K.321, C.322, S.323, T.476, G.477, A.478, F.485 Ligands: NAD.8 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.185, B:F.185 Hydrogen bonds: B:N.184, B:C.322, B:S.323, B:S.323, B:S.323, B:G.477, B:A.478 Water bridges: B:E.137, B:E.137 FLC.17: 11 residues within 4Å: Chain C: E.137, N.184, F.185, K.321, C.322, S.323, T.476, G.477, A.478, F.485 Ligands: NAD.16 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.185, C:F.185 Hydrogen bonds: C:N.184, C:C.322, C:S.323, C:S.323, C:S.323, C:G.477, C:A.478 Water bridges: C:E.137 FLC.24: 11 residues within 4Å: Chain D: E.137, N.184, F.185, K.321, C.322, S.323, T.476, G.477, A.478, F.485 Ligands: NAD.23 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.185, D:F.185 Hydrogen bonds: D:N.184, D:C.322, D:S.323, D:S.323, D:S.323, D:G.477, D:A.478 Water bridges: D:E.137, D:E.137 FLC.32: 11 residues within 4Å: Chain E: E.137, N.184, F.185, K.321, C.322, S.323, T.476, G.477, A.478, F.485 Ligands: NAD.31 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.185, E:F.185 Hydrogen bonds: E:N.184, E:C.322, E:S.323, E:S.323, E:S.323, E:G.477, E:A.478 Water bridges: E:E.137 FLC.39: 11 residues within 4Å: Chain F: E.137, N.184, F.185, K.321, C.322, S.323, T.476, G.477, A.478, F.485 Ligands: NAD.38 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:F.185, F:F.185 Hydrogen bonds: F:N.184, F:C.322, F:S.323, F:S.323, F:S.323, F:G.477, F:A.478 Water bridges: F:E.137, F:E.137

12 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 6 residues within 4Å: Chain A: L.275, G.278, Q.279, T.280 Chain B: P.442, L.490 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.275, A:T.280, B:P.442, B:L.490 Hydrogen bonds: A:G.278 MRD.10: 4 residues within 4Å: Chain B: R.151, A.156, Y.171, L.500 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.171, B:L.500 Water bridges: B:Y.171, A:D.501 MRD.12: 5 residues within 4Å: Chain A: P.442, L.490 Chain B: L.275, G.278, Q.279 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.442, A:L.490, B:L.275 Hydrogen bonds: B:G.278 MRD.14: 3 residues within 4Å: Chain B: P.353, E.355, E.356 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.355 MRD.18: 6 residues within 4Å: Chain C: L.275, G.278, Q.279, T.280 Chain D: P.442, L.490 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.275, C:T.280, D:P.442, D:L.490 Hydrogen bonds: C:G.278 MRD.25: 4 residues within 4Å: Chain D: R.151, A.156, Y.171, L.500 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.171, D:L.500 Water bridges: D:Y.171, C:D.501 MRD.27: 5 residues within 4Å: Chain C: P.442, L.490 Chain D: L.275, G.278, Q.279 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.442, C:L.490, D:L.275 Hydrogen bonds: D:G.278 MRD.29: 3 residues within 4Å: Chain D: P.353, E.355, E.356 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:E.355 MRD.33: 6 residues within 4Å: Chain E: L.275, G.278, Q.279, T.280 Chain F: P.442, L.490 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:L.275, E:T.280, F:P.442, F:L.490 Hydrogen bonds: E:G.278 MRD.40: 4 residues within 4Å: Chain F: R.151, A.156, Y.171, L.500 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:Y.171, F:L.500 Water bridges: F:Y.171, E:D.501 MRD.42: 5 residues within 4Å: Chain E: P.442, L.490 Chain F: L.275, G.278, Q.279 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:P.442, E:L.490, F:L.275 Hydrogen bonds: F:G.278 MRD.44: 3 residues within 4Å: Chain F: P.353, E.355, E.356 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:E.355

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

MPD.4: 6 residues within 4Å: Chain A: F.6, Y.144, R.147, A.148, L.500 Chain B: E.158 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Water bridges: B:E.158 Hydrophobic interactions: A:F.6, A:Y.144, A:R.147, A:A.148, A:L.500 MPD.5: 4 residues within 4Å: Chain A: V.312, Y.315, G.316, D.359 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.312 Hydrogen bonds: A:E.308 Water bridges: A:V.312 MPD.6: 4 residues within 4Å: Chain A: R.36, P.39, W.46, E.221 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.46, A:W.46, A:E.221 Hydrogen bonds: A:R.36 MPD.11: 6 residues within 4Å: Chain A: E.158 Chain B: F.6, Y.144, R.147, A.148, L.500 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.6, B:Y.144, B:R.147, B:A.148, B:L.500 Hydrogen bonds: A:E.158 MPD.13: 4 residues within 4Å: Chain B: R.36, Y.38, W.46, E.221 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.38, B:W.46, B:W.46, B:E.221 Hydrogen bonds: B:R.36, B:E.221, B:E.221 MPD.19: 6 residues within 4Å: Chain C: F.6, Y.144, R.147, A.148, L.500 Chain D: E.158 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.6, C:Y.144, C:R.147, C:A.148, C:L.500 Water bridges: D:E.158 MPD.20: 4 residues within 4Å: Chain C: V.312, Y.315, G.316, D.359 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.312 Hydrogen bonds: C:E.308 Water bridges: C:V.312 MPD.21: 4 residues within 4Å: Chain C: R.36, P.39, W.46, E.221 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.46, C:W.46, C:E.221 Hydrogen bonds: C:R.36 MPD.26: 6 residues within 4Å: Chain C: E.158 Chain D: F.6, Y.144, R.147, A.148, L.500 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:E.158 Hydrophobic interactions: D:F.6, D:Y.144, D:R.147, D:A.148, D:L.500 MPD.28: 4 residues within 4Å: Chain D: R.36, Y.38, W.46, E.221 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.38, D:W.46, D:W.46, D:E.221 Hydrogen bonds: D:R.36, D:E.221, D:E.221 MPD.34: 6 residues within 4Å: Chain E: F.6, Y.144, R.147, A.148, L.500 Chain F: E.158 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:F.6, E:Y.144, E:R.147, E:A.148, E:L.500 Water bridges: F:E.158 MPD.35: 4 residues within 4Å: Chain E: V.312, Y.315, G.316, D.359 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.312 Hydrogen bonds: E:E.308 Water bridges: E:V.312 MPD.36: 4 residues within 4Å: Chain E: R.36, P.39, W.46, E.221 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:W.46, E:W.46, E:E.221 Hydrogen bonds: E:R.36 MPD.41: 6 residues within 4Å: Chain E: E.158 Chain F: F.6, Y.144, R.147, A.148, L.500 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:F.6, F:Y.144, F:R.147, F:A.148, F:L.500 Hydrogen bonds: E:E.158 MPD.43: 4 residues within 4Å: Chain F: R.36, Y.38, W.46, E.221 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:Y.38, F:W.46, F:W.46, F:E.221 Hydrogen bonds: F:R.36, F:E.221, F:E.221

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

CL.7: 4 residues within 4Å: Chain A: R.462, H.465, F.488 Chain B: K.510 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: K.510 Chain B: H.465, F.488 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain C: R.462, H.465, F.488 Chain D: K.510 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain C: K.510 Chain D: H.465, F.488 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain E: R.462, H.465, F.488 Chain F: K.510 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain E: K.510 Chain F: H.465, F.488 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inagaki, E. et al., Crystal Structure of Thermus Thermophilus Delta(1)- Pyrroline-5-Carboxylate Dehydrogenase. J.Mol.Biol. (2006)

Release Date

2006-03-09

Peptides

1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE

Related Entries With Identical Sequence