SMTL ID : 2j5n.1

1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS THERMOPHIRUS WITH BOUND INHIBITOR GLYCINE AND NAD.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-hexamer

Ligands

6 x GLY: GLYCINE(Non-covalent)

GLY.1: 5 residues within 4Å: Chain A: S.323, T.476, G.477, A.478, F.485 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.323, A:G.477, A:A.478 Water bridges: A:E.137 GLY.10: 5 residues within 4Å: Chain B: S.323, T.476, G.477, A.478, F.485 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.323, B:G.477, B:A.478 Water bridges: B:E.137 GLY.20: 5 residues within 4Å: Chain C: S.323, T.476, G.477, A.478, F.485 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.323, C:G.477, C:A.478 Water bridges: C:E.137 GLY.29: 5 residues within 4Å: Chain D: S.323, T.476, G.477, A.478, F.485 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.323, D:G.477, D:A.478 Water bridges: D:E.137 GLY.39: 5 residues within 4Å: Chain E: S.323, T.476, G.477, A.478, F.485 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.323, E:G.477, E:A.478 Water bridges: E:E.137 GLY.48: 5 residues within 4Å: Chain F: S.323, T.476, G.477, A.478, F.485 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:S.323, F:G.477, F:A.478 Water bridges: F:E.137

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

NAD.2: 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: ACT.3 22 PLIP interactions: 22 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:S.261, A:T.289, A:E.417 Water bridges: A:W.183, A:E.241, A:E.241, A:E.241, A:K.267, A:G.290, A:K.371, A:K.371, A:E.417, A:E.417 NAD.11: 29 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, I.268, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485 Ligands: ACT.12 19 PLIP interactions: 19 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:E.241, B:S.261, B:K.267, B:K.267, B:E.288, B:G.290, B:E.417 NAD.21: 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: ACT.22 22 PLIP interactions: 22 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:S.261, C:T.289, C:E.417 Water bridges: C:W.183, C:E.241, C:E.241, C:E.241, C:K.267, C:G.290, C:K.371, C:K.371, C:E.417, C:E.417 NAD.30: 29 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, I.268, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485 Ligands: ACT.31 19 PLIP interactions: 19 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:E.241, D:S.261, D:K.267, D:K.267, D:E.288, D:G.290, D:E.417 NAD.40: 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: ACT.41 22 PLIP interactions: 22 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:S.261, E:T.289, E:E.417 Water bridges: E:W.183, E:E.241, E:E.241, E:E.241, E:K.267, E:G.290, E:K.371, E:K.371, E:E.417, E:E.417 NAD.49: 29 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, I.268, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485 Ligands: ACT.50 19 PLIP interactions: 19 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:E.241, F:S.261, F:K.267, F:K.267, F:E.288, F:G.290, F:E.417

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 7 residues within 4Å: Chain A: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAD.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.271 ACT.4: 6 residues within 4Å: Chain A: R.461, R.462, F.464, H.465 Chain B: V.172, K.510 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:R.462 Salt bridges: A:H.465, B:K.510 Hydrophobic interactions: B:V.172, B:K.510 ACT.12: 7 residues within 4Å: Chain B: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAD.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.271 Water bridges: B:K.267 ACT.13: 6 residues within 4Å: Chain A: V.172, K.510 Chain B: R.461, R.462, F.464, H.465 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.172, A:K.510 Salt bridges: A:K.510, B:H.465 Hydrogen bonds: B:F.464 ACT.22: 7 residues within 4Å: Chain C: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAD.21 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.271 ACT.23: 6 residues within 4Å: Chain C: R.461, R.462, F.464, H.465 Chain D: V.172, K.510 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.172, D:K.510 Salt bridges: D:K.510, C:H.465 Water bridges: C:R.462 ACT.31: 7 residues within 4Å: Chain D: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAD.30 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.271 Water bridges: D:K.267 ACT.32: 6 residues within 4Å: Chain C: V.172, K.510 Chain D: R.461, R.462, F.464, H.465 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:F.464 Salt bridges: D:H.465, C:K.510 Hydrophobic interactions: C:V.172, C:K.510 ACT.41: 7 residues within 4Å: Chain E: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAD.40 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.271 ACT.42: 6 residues within 4Å: Chain E: R.461, R.462, F.464, H.465 Chain F: V.172, K.510 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:V.172, F:K.510 Salt bridges: F:K.510, E:H.465 Water bridges: E:R.462 ACT.50: 7 residues within 4Å: Chain F: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAD.49 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:A.271 Water bridges: F:K.267 ACT.51: 6 residues within 4Å: Chain E: V.172, K.510 Chain F: R.461, R.462, F.464, H.465 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:V.172, E:K.510 Salt bridges: E:K.510, F:H.465 Hydrogen bonds: F:F.464

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

MRD.5: 6 residues within 4Å: Chain A: L.275, G.278, Q.279, T.280 Chain B: P.442, L.490 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.442, B:L.490, A:L.275, A:T.280 Hydrogen bonds: A:G.278 MRD.15: 7 residues within 4Å: Chain A: E.158, V.160 Chain B: F.6, Y.144, R.147, A.148, L.500 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.160, B:F.6, B:Y.144, B:Y.144, B:R.147, B:A.148, B:L.500 Hydrogen bonds: A:E.158, A:E.158 MRD.16: 6 residues within 4Å: Chain A: P.442, L.490 Chain B: L.275, G.278, Q.279, T.280 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.442, A:L.490, B:L.275, B:T.280 Hydrogen bonds: B:G.278 MRD.24: 6 residues within 4Å: Chain C: L.275, G.278, Q.279, T.280 Chain D: P.442, L.490 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:P.442, D:L.490, C:L.275, C:T.280 Hydrogen bonds: C:G.278 MRD.34: 7 residues within 4Å: Chain C: E.158, V.160 Chain D: F.6, Y.144, R.147, A.148, L.500 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.6, D:Y.144, D:Y.144, D:R.147, D:A.148, D:L.500, C:V.160 Hydrogen bonds: C:E.158, C:E.158 MRD.35: 6 residues within 4Å: Chain C: P.442, L.490 Chain D: L.275, G.278, Q.279, T.280 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.275, D:T.280, C:P.442, C:L.490 Hydrogen bonds: D:G.278 MRD.43: 6 residues within 4Å: Chain E: L.275, G.278, Q.279, T.280 Chain F: P.442, L.490 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:P.442, F:L.490, E:L.275, E:T.280 Hydrogen bonds: E:G.278 MRD.53: 7 residues within 4Å: Chain E: E.158, V.160 Chain F: F.6, Y.144, R.147, A.148, L.500 9 PLIP interactions: 6 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:F.6, F:Y.144, F:Y.144, F:R.147, F:A.148, F:L.500, E:V.160 Hydrogen bonds: E:E.158, E:E.158 MRD.54: 6 residues within 4Å: Chain E: P.442, L.490 Chain F: L.275, G.278, Q.279, T.280 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:L.275, F:T.280, E:P.442, E:L.490 Hydrogen bonds: F:G.278

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

MPD.6: 6 residues within 4Å: Chain A: F.6, Y.144, R.147, A.148, L.500 Chain B: E.158 Ligand excluded by PLIP MPD.7: 5 residues within 4Å: Chain A: R.151, Y.152, Y.171, L.500 Ligands: MPD.14 Ligand excluded by PLIP MPD.8: 4 residues within 4Å: Chain A: R.36, P.39, W.46, E.221 Ligand excluded by PLIP MPD.14: 6 residues within 4Å: Chain B: R.151, Y.152, A.156, Y.171, L.500 Ligands: MPD.7 Ligand excluded by PLIP MPD.17: 4 residues within 4Å: Chain B: R.36, Y.38, W.46, E.221 Ligand excluded by PLIP MPD.18: 3 residues within 4Å: Chain B: P.353, E.355, E.356 Ligand excluded by PLIP MPD.25: 6 residues within 4Å: Chain C: F.6, Y.144, R.147, A.148, L.500 Chain D: E.158 Ligand excluded by PLIP MPD.26: 5 residues within 4Å: Chain C: R.151, Y.152, Y.171, L.500 Ligands: MPD.33 Ligand excluded by PLIP MPD.27: 4 residues within 4Å: Chain C: R.36, P.39, W.46, E.221 Ligand excluded by PLIP MPD.33: 6 residues within 4Å: Chain D: R.151, Y.152, A.156, Y.171, L.500 Ligands: MPD.26 Ligand excluded by PLIP MPD.36: 4 residues within 4Å: Chain D: R.36, Y.38, W.46, E.221 Ligand excluded by PLIP MPD.37: 3 residues within 4Å: Chain D: P.353, E.355, E.356 Ligand excluded by PLIP MPD.44: 6 residues within 4Å: Chain E: F.6, Y.144, R.147, A.148, L.500 Chain F: E.158 Ligand excluded by PLIP MPD.45: 5 residues within 4Å: Chain E: R.151, Y.152, Y.171, L.500 Ligands: MPD.52 Ligand excluded by PLIP MPD.46: 4 residues within 4Å: Chain E: R.36, P.39, W.46, E.221 Ligand excluded by PLIP MPD.52: 6 residues within 4Å: Chain F: R.151, Y.152, A.156, Y.171, L.500 Ligands: MPD.45 Ligand excluded by PLIP MPD.55: 4 residues within 4Å: Chain F: R.36, Y.38, W.46, E.221 Ligand excluded by PLIP MPD.56: 3 residues within 4Å: Chain F: P.353, E.355, E.356 Ligand excluded by PLIP

6 x NA: SODIUM ION(Non-functional Binders)

NA.9: 4 residues within 4Å: Chain A: S.55, L.56, E.123, D.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.56, A:E.123 NA.19: 4 residues within 4Å: Chain B: S.55, L.56, E.123, D.211 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.56, B:E.123 Water bridges: B:D.211 NA.28: 4 residues within 4Å: Chain C: S.55, L.56, E.123, D.211 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.56, C:D.211 NA.38: 4 residues within 4Å: Chain D: S.55, L.56, E.123, D.211 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.56, D:L.56 Water bridges: D:D.211 NA.47: 4 residues within 4Å: Chain E: S.55, L.56, E.123, D.211 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.55, E:L.56 NA.57: 4 residues within 4Å: Chain F: S.55, L.56, E.123, D.211 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:L.56, F:D.211 Water bridges: F:D.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inagaki, E. et al., Crystal Structure of Ternary Complex of Delta1-Pyrroline-5-Carboxylate Dehydrogenase with Substrate Mimic and Co-Factoer. To be Published

Release Date

2007-10-16

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

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