SMTL ID : 2eiw.2 (1 other biounit)

Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound L-proline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

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

ACT.1: 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.9: 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.17: 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 Hydrogen bonds: C:F.464 ACT.25: 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.33: 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.41: 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 NA: SODIUM ION(Non-functional Binders)

NA.2: 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:S.55, A:L.56 NA.10: 4 residues within 4Å: Chain B: S.55, L.56, E.123, D.211 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.56, B:E.123 NA.18: 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.26: 4 residues within 4Å: Chain D: S.55, L.56, E.123, D.211 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.56, D:D.211 NA.34: 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:E.123 NA.42: 4 residues within 4Å: Chain F: S.55, L.56, E.123, D.211 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:L.56, F:D.211

6 x PRO: PROLINE(Non-covalent)

PRO.3: 8 residues within 4Å: Chain A: E.137, F.185, I.189, S.323, T.476, G.477, A.478, F.485 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.185, A:I.189, A:F.485 Hydrogen bonds: A:S.323, A:G.477, A:A.478, A:A.478, P.3 Water bridges: A:K.321 PRO.11: 8 residues within 4Å: Chain B: E.137, F.185, I.189, S.323, T.476, G.477, A.478, F.485 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.185, B:I.189, B:F.485 Hydrogen bonds: B:S.323, B:G.477, B:A.478, B:A.478, P.11 PRO.19: 8 residues within 4Å: Chain C: E.137, F.185, I.189, S.323, T.476, G.477, A.478, F.485 9 PLIP interactions: 8 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:F.185, C:I.189, C:F.485 Hydrogen bonds: C:S.323, C:G.477, C:A.478, C:A.478, P.19 Water bridges: C:K.321 PRO.27: 8 residues within 4Å: Chain D: E.137, F.185, I.189, S.323, T.476, G.477, A.478, F.485 8 PLIP interactions: 7 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:F.185, D:I.189, D:F.485 Hydrogen bonds: D:S.323, D:G.477, D:A.478, D:A.478, P.27 PRO.35: 8 residues within 4Å: Chain E: E.137, F.185, I.189, S.323, T.476, G.477, A.478, F.485 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain E Hydrogen bonds: P.35, E:S.323, E:G.477, E:A.478, E:A.478 Hydrophobic interactions: E:F.185, E:I.189, E:F.485 Water bridges: E:K.321 PRO.43: 8 residues within 4Å: Chain F: E.137, F.185, I.189, S.323, T.476, G.477, A.478, F.485 8 PLIP interactions: 7 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: F:F.185, F:I.189, F:F.485 Hydrogen bonds: F:S.323, F:G.477, F:A.478, F:A.478, P.43

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

MPD.4: 5 residues within 4Å: Chain A: V.311, V.312, Y.315, G.316, D.359 Ligand excluded by PLIP MPD.5: 5 residues within 4Å: Chain A: I.180, E.241, G.244, A.245, V.264 Ligand excluded by PLIP MPD.6: 3 residues within 4Å: Chain A: L.262, E.263, E.416 Ligand excluded by PLIP MPD.7: 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.8: 4 residues within 4Å: Chain A: R.151, A.156, Y.171, L.500 Ligand excluded by PLIP MPD.12: 6 residues within 4Å: Chain A: Y.144, R.147, A.148, L.500 Chain B: E.158, V.160 Ligand excluded by PLIP MPD.13: 5 residues within 4Å: Chain B: R.151, Y.152, A.156, Y.171, L.500 Ligand excluded by PLIP MPD.14: 7 residues within 4Å: Chain B: I.180, E.241, G.244, A.245, V.264, K.267, I.268 Ligand excluded by PLIP MPD.15: 3 residues within 4Å: Chain B: P.353, E.355, E.356 Ligand excluded by PLIP MPD.16: 6 residues within 4Å: Chain B: V.311, V.312, Y.315, G.316, L.349, D.359 Ligand excluded by PLIP MPD.20: 5 residues within 4Å: Chain C: V.311, V.312, Y.315, G.316, D.359 Ligand excluded by PLIP MPD.21: 5 residues within 4Å: Chain C: I.180, E.241, G.244, A.245, V.264 Ligand excluded by PLIP MPD.22: 3 residues within 4Å: Chain C: L.262, E.263, E.416 Ligand excluded by PLIP MPD.23: 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.24: 4 residues within 4Å: Chain C: R.151, A.156, Y.171, L.500 Ligand excluded by PLIP MPD.28: 6 residues within 4Å: Chain C: Y.144, R.147, A.148, L.500 Chain D: E.158, V.160 Ligand excluded by PLIP MPD.29: 5 residues within 4Å: Chain D: R.151, Y.152, A.156, Y.171, L.500 Ligand excluded by PLIP MPD.30: 7 residues within 4Å: Chain D: I.180, E.241, G.244, A.245, V.264, K.267, I.268 Ligand excluded by PLIP MPD.31: 3 residues within 4Å: Chain D: P.353, E.355, E.356 Ligand excluded by PLIP MPD.32: 6 residues within 4Å: Chain D: V.311, V.312, Y.315, G.316, L.349, D.359 Ligand excluded by PLIP MPD.36: 5 residues within 4Å: Chain E: V.311, V.312, Y.315, G.316, D.359 Ligand excluded by PLIP MPD.37: 5 residues within 4Å: Chain E: I.180, E.241, G.244, A.245, V.264 Ligand excluded by PLIP MPD.38: 3 residues within 4Å: Chain E: L.262, E.263, E.416 Ligand excluded by PLIP MPD.39: 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.40: 4 residues within 4Å: Chain E: R.151, A.156, Y.171, L.500 Ligand excluded by PLIP MPD.44: 6 residues within 4Å: Chain E: Y.144, R.147, A.148, L.500 Chain F: E.158, V.160 Ligand excluded by PLIP MPD.45: 5 residues within 4Å: Chain F: R.151, Y.152, A.156, Y.171, L.500 Ligand excluded by PLIP MPD.46: 7 residues within 4Å: Chain F: I.180, E.241, G.244, A.245, V.264, K.267, I.268 Ligand excluded by PLIP MPD.47: 3 residues within 4Å: Chain F: P.353, E.355, E.356 Ligand excluded by PLIP MPD.48: 6 residues within 4Å: Chain F: V.311, V.312, Y.315, G.316, L.349, 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

2007-09-18

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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