SMTL ID : 2ehu.2 (2 other biounits)

Crystal analysis of 1-pyrroline-5-carboxylate dehydrogenase from thermus with bound NAD and Inhibitor L-serine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

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

NA.1: 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.14: 5 residues within 4Å: Chain B: S.55, L.56, P.58, E.123, D.211 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.56, B:L.56 Water bridges: B:D.211 NA.24: 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:S.55, C:L.56 NA.37: 5 residues within 4Å: Chain D: S.55, L.56, P.58, 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:L.56, E:D.211 NA.60: 5 residues within 4Å: Chain F: S.55, L.56, P.58, E.123, D.211 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.55, F:L.56 Water bridges: F:D.211

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

ACT.2: 7 residues within 4Å: Chain A: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAD.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.249, A:A.271 ACT.3: 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 Hydrogen bonds: A:F.464 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.16 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.248, B:A.271 Water bridges: B:K.267, 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 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.172, A:K.510 Salt bridges: A:K.510, B:H.465 ACT.25: 7 residues within 4Å: Chain C: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAD.28 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.249, C:A.271 ACT.26: 6 residues within 4Å: Chain C: R.461, R.462, F.464, H.465 Chain D: V.172, K.510 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:F.464 Salt bridges: C:H.465, D:K.510 Hydrophobic interactions: D:V.172, D:K.510 ACT.35: 7 residues within 4Å: Chain D: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAD.39 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.248, D:A.271 Water bridges: D:K.267, D:K.267 ACT.36: 6 residues within 4Å: Chain C: V.172, K.510 Chain D: R.461, R.462, F.464, H.465 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.172, C:K.510 Salt bridges: C:K.510, D:H.465 ACT.48: 7 residues within 4Å: Chain E: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAD.51 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.249, E:A.271 ACT.49: 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 Hydrogen bonds: E:F.464 ACT.58: 7 residues within 4Å: Chain F: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAD.62 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:V.248, F:A.271 Water bridges: F:K.267, F:K.267 ACT.59: 6 residues within 4Å: Chain E: V.172, K.510 Chain F: R.461, R.462, F.464, H.465 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:V.172, E:K.510 Salt bridges: E:K.510, F:H.465

6 x SER: SERINE(Non-covalent)

SER.4: 8 residues within 4Å: Chain A: F.185, K.321, C.322, S.323, T.476, G.477, A.478, F.485 10 PLIP interactions: 2 Ligand-Ligand interactions, 8 interactions with chain A Hydrogen bonds: S.4, S.4, A:C.322, A:S.323, A:S.323, A:G.477, A:A.478 Water bridges: A:E.137, A:E.137, A:A.478 SER.15: 7 residues within 4Å: Chain B: F.185, C.322, S.323, T.476, G.477, A.478, F.485 9 PLIP interactions: 8 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:C.322, B:S.323, B:S.323, B:G.477, B:A.478 Water bridges: B:E.137, B:E.137, B:A.478, S.15 SER.27: 8 residues within 4Å: Chain C: F.185, K.321, C.322, S.323, T.476, G.477, A.478, F.485 10 PLIP interactions: 8 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:C.322, C:S.323, C:S.323, C:G.477, C:A.478, S.27, S.27 Water bridges: C:E.137, C:E.137, C:A.478 SER.38: 7 residues within 4Å: Chain D: F.185, C.322, S.323, T.476, G.477, A.478, F.485 9 PLIP interactions: 8 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:C.322, D:S.323, D:S.323, D:G.477, D:A.478 Water bridges: D:E.137, D:E.137, D:A.478, S.38 SER.50: 8 residues within 4Å: Chain E: F.185, K.321, C.322, S.323, T.476, G.477, A.478, F.485 10 PLIP interactions: 8 interactions with chain E, 2 Ligand-Ligand interactions Hydrogen bonds: E:C.322, E:S.323, E:S.323, E:G.477, E:A.478, S.50, S.50 Water bridges: E:E.137, E:E.137, E:A.478 SER.61: 7 residues within 4Å: Chain F: F.185, C.322, S.323, T.476, G.477, A.478, F.485 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain F Water bridges: S.61, F:E.137, F:E.137, F:A.478 Hydrogen bonds: F:C.322, F:S.323, F:S.323, F:G.477, F:A.478

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

NAD.5: 29 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, I.268, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485 Ligands: ACT.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:E.241, A:S.261, A:T.289, A:E.417 Water bridges: A:W.183, A:S.261, A:G.290, A:E.417, A:E.417 NAD.16: 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 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:E.241, B:S.261, B:K.267, B:K.267, B:E.288, B:E.288, B:G.290 NAD.28: 29 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, I.268, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485 Ligands: ACT.25 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:E.241, C:S.261, C:T.289, C:E.417 Water bridges: C:W.183, C:S.261, C:G.290, C:E.417, C:E.417 NAD.39: 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.35 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:E.241, D:S.261, D:K.267, D:K.267, D:E.288, D:E.288, D:G.290 NAD.51: 29 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, I.268, E.288, T.289, G.290, C.322, E.417, F.419, L.445, F.485 Ligands: ACT.48 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:E.241, E:S.261, E:T.289, E:E.417 Water bridges: E:W.183, E:S.261, E:G.290, E:E.417, E:E.417 NAD.62: 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.58 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:E.241, F:S.261, F:K.267, F:K.267, F:E.288, F:E.288, F:G.290

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

MPD.6: 4 residues within 4Å: Chain A: V.312, Y.315, G.316, D.359 Ligand excluded by PLIP MPD.7: 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.8: 4 residues within 4Å: Chain A: Y.154, F.170 Chain B: R.462 Chain D: P.94 Ligand excluded by PLIP MPD.9: 5 residues within 4Å: Chain A: R.36, Y.38, P.39, W.46, E.221 Ligand excluded by PLIP MPD.10: 6 residues within 4Å: Chain A: L.275, G.278, Q.279, T.280 Chain B: P.442, L.490 Ligand excluded by PLIP MPD.11: 5 residues within 4Å: Chain A: R.151, A.156, Y.171, L.500 Ligands: MPD.17 Ligand excluded by PLIP MPD.17: 6 residues within 4Å: Chain B: R.151, Y.152, A.156, Y.171, L.500 Ligands: MPD.11 Ligand excluded by PLIP MPD.18: 6 residues within 4Å: Chain A: E.158 Chain B: F.6, Y.144, R.147, A.148, L.500 Ligand excluded by PLIP MPD.19: 4 residues within 4Å: Chain A: R.462 Chain B: Y.154, F.170 Chain E: P.94 Ligand excluded by PLIP MPD.20: 3 residues within 4Å: Chain B: P.353, E.355, E.356 Ligand excluded by PLIP MPD.21: 5 residues within 4Å: Chain A: P.442 Chain B: L.275, G.278, Q.279, T.280 Ligand excluded by PLIP MPD.22: 4 residues within 4Å: Chain B: R.36, Y.38, W.46, E.221 Ligand excluded by PLIP MPD.23: 4 residues within 4Å: Chain B: V.312, Y.315, G.316, D.359 Ligand excluded by PLIP MPD.29: 4 residues within 4Å: Chain C: V.312, Y.315, G.316, D.359 Ligand excluded by PLIP MPD.30: 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.31: 4 residues within 4Å: Chain C: Y.154, F.170 Chain D: R.462 Chain F: P.94 Ligand excluded by PLIP MPD.32: 5 residues within 4Å: Chain C: R.36, Y.38, P.39, W.46, E.221 Ligand excluded by PLIP MPD.33: 6 residues within 4Å: Chain C: L.275, G.278, Q.279, T.280 Chain D: P.442, L.490 Ligand excluded by PLIP MPD.34: 5 residues within 4Å: Chain C: R.151, A.156, Y.171, L.500 Ligands: MPD.40 Ligand excluded by PLIP MPD.40: 6 residues within 4Å: Chain D: R.151, Y.152, A.156, Y.171, L.500 Ligands: MPD.34 Ligand excluded by PLIP MPD.41: 6 residues within 4Å: Chain C: E.158 Chain D: F.6, Y.144, R.147, A.148, L.500 Ligand excluded by PLIP MPD.42: 4 residues within 4Å: Chain A: P.94 Chain C: R.462 Chain D: Y.154, F.170 Ligand excluded by PLIP MPD.43: 3 residues within 4Å: Chain D: P.353, E.355, E.356 Ligand excluded by PLIP MPD.44: 5 residues within 4Å: Chain C: P.442 Chain D: L.275, G.278, Q.279, T.280 Ligand excluded by PLIP MPD.45: 4 residues within 4Å: Chain D: R.36, Y.38, W.46, E.221 Ligand excluded by PLIP MPD.46: 4 residues within 4Å: Chain D: V.312, Y.315, G.316, D.359 Ligand excluded by PLIP MPD.52: 4 residues within 4Å: Chain E: V.312, Y.315, G.316, D.359 Ligand excluded by PLIP MPD.53: 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.54: 4 residues within 4Å: Chain B: P.94 Chain E: Y.154, F.170 Chain F: R.462 Ligand excluded by PLIP MPD.55: 5 residues within 4Å: Chain E: R.36, Y.38, P.39, W.46, E.221 Ligand excluded by PLIP MPD.56: 6 residues within 4Å: Chain E: L.275, G.278, Q.279, T.280 Chain F: P.442, L.490 Ligand excluded by PLIP MPD.57: 5 residues within 4Å: Chain E: R.151, A.156, Y.171, L.500 Ligands: MPD.63 Ligand excluded by PLIP MPD.63: 6 residues within 4Å: Chain F: R.151, Y.152, A.156, Y.171, L.500 Ligands: MPD.57 Ligand excluded by PLIP MPD.64: 6 residues within 4Å: Chain E: E.158 Chain F: F.6, Y.144, R.147, A.148, L.500 Ligand excluded by PLIP MPD.65: 4 residues within 4Å: Chain C: P.94 Chain E: R.462 Chain F: Y.154, F.170 Ligand excluded by PLIP MPD.66: 3 residues within 4Å: Chain F: P.353, E.355, E.356 Ligand excluded by PLIP MPD.67: 5 residues within 4Å: Chain E: P.442 Chain F: L.275, G.278, Q.279, T.280 Ligand excluded by PLIP MPD.68: 4 residues within 4Å: Chain F: R.36, Y.38, W.46, E.221 Ligand excluded by PLIP MPD.69: 4 residues within 4Å: Chain F: V.312, Y.315, G.316, D.359 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inagaki, E. et al., Crystal Structure Analysis of delta1-pyrroline-5-carboxylate dehydrogenase in ternary complex with inhibitor and NAD. To be Published

Release Date

2007-09-11

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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