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

Crystal analysis of 1-pyrroline-5-carboxylate dehydrogenase from thermus with bound NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-hexamer

Ligands

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

ACT.1: 7 residues within 4Å: Chain A: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAP.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.271 ACT.2: 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.8: 7 residues within 4Å: Chain B: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAP.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.248, B:A.271 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: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:H.465, A:K.510 Hydrophobic interactions: A:V.172, A:K.510 ACT.16: 7 residues within 4Å: Chain C: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAP.19 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.271 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.23: 7 residues within 4Å: Chain D: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAP.26 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.248, D:A.271 ACT.24: 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.31: 7 residues within 4Å: Chain E: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAP.34 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.271 ACT.32: 6 residues within 4Å: Chain E: R.461, R.462, F.464, H.465 Chain F: V.172, K.510 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:F.464 Salt bridges: E:H.465, F:K.510 Hydrophobic interactions: F:V.172, F:K.510 ACT.38: 7 residues within 4Å: Chain F: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAP.41 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:V.248, F:A.271 ACT.39: 6 residues within 4Å: Chain E: V.172, K.510 Chain F: R.461, R.462, F.464, H.465 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Salt bridges: F:H.465, E:K.510 Hydrophobic interactions: E:V.172, E:K.510

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

NA.3: 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: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:L.56, C:D.211 NA.25: 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.33: 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.40: 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 NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.4: 31 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.238, V.239, 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.1 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:P.182, A:I.189, A:T.259 Hydrogen bonds: A:A.181, A:A.181, A:W.183, A:K.207, A:E.210, A:E.210, A:G.238, A:G.240, A:S.261, A:T.289, A:E.417 Water bridges: A:W.183, A:W.183, A:W.183, A:D.211, A:E.241, A:E.241, A:G.290, A:Q.368, A:E.417, A:E.417 Salt bridges: A:K.207 NAP.11: 31 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.238, V.239, 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.8 22 PLIP interactions: 22 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.238, B:G.240, B:S.261, B:T.289, B:E.417 Water bridges: B:W.183, B:D.211, B:E.241, B:E.241, B:E.288, B:E.288, B:G.290, B:Q.368, B:E.417 Salt bridges: B:K.207 NAP.19: 31 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.238, V.239, 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.16 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:P.182, C:I.189, C:T.259 Hydrogen bonds: C:A.181, C:A.181, C:W.183, C:K.207, C:E.210, C:E.210, C:G.238, C:G.240, C:S.261, C:T.289, C:E.417 Water bridges: C:W.183, C:W.183, C:W.183, C:D.211, C:E.241, C:E.241, C:G.290, C:Q.368, C:E.417, C:E.417 Salt bridges: C:K.207 NAP.26: 31 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.238, V.239, 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.23 22 PLIP interactions: 22 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.238, D:G.240, D:S.261, D:T.289, D:E.417 Water bridges: D:W.183, D:D.211, D:E.241, D:E.241, D:E.288, D:E.288, D:G.290, D:Q.368, D:E.417 Salt bridges: D:K.207 NAP.34: 31 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.238, V.239, 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 25 PLIP interactions: 25 interactions with chain E Hydrophobic interactions: E:P.182, E:I.189, E:T.259 Hydrogen bonds: E:A.181, E:A.181, E:W.183, E:K.207, E:E.210, E:E.210, E:G.238, E:G.240, E:S.261, E:T.289, E:E.417 Water bridges: E:W.183, E:W.183, E:W.183, E:D.211, E:E.241, E:E.241, E:G.290, E:Q.368, E:E.417, E:E.417 Salt bridges: E:K.207 NAP.41: 31 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.238, V.239, 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.38 22 PLIP interactions: 22 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.238, F:G.240, F:S.261, F:T.289, F:E.417 Water bridges: F:W.183, F:D.211, F:E.241, F:E.241, F:E.288, F:E.288, F:G.290, F:Q.368, F:E.417 Salt bridges: F:K.207

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

MPD.5: 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.6: 5 residues within 4Å: Chain A: R.151, Y.152, Y.171, L.500 Ligands: MPD.12 Ligand excluded by PLIP MPD.7: 3 residues within 4Å: Chain A: E.308, V.312, D.359 Ligand excluded by PLIP MPD.12: 6 residues within 4Å: Chain B: R.151, Y.152, A.156, Y.171, L.500 Ligands: MPD.6 Ligand excluded by PLIP MPD.13: 7 residues within 4Å: Chain A: E.158, V.160 Chain B: F.6, Y.144, R.147, A.148, L.500 Ligand excluded by PLIP MPD.14: 6 residues within 4Å: Chain A: P.442, L.490 Chain B: L.275, G.278, Q.279, T.280 Ligand excluded by PLIP MPD.15: 3 residues within 4Å: Chain B: P.353, E.355, E.356 Ligand excluded by PLIP MPD.20: 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.21: 5 residues within 4Å: Chain C: R.151, Y.152, Y.171, L.500 Ligands: MPD.27 Ligand excluded by PLIP MPD.22: 3 residues within 4Å: Chain C: E.308, V.312, D.359 Ligand excluded by PLIP MPD.27: 6 residues within 4Å: Chain D: R.151, Y.152, A.156, Y.171, L.500 Ligands: MPD.21 Ligand excluded by PLIP MPD.28: 7 residues within 4Å: Chain C: E.158, V.160 Chain D: F.6, Y.144, R.147, A.148, L.500 Ligand excluded by PLIP MPD.29: 6 residues within 4Å: Chain C: P.442, L.490 Chain D: L.275, G.278, Q.279, T.280 Ligand excluded by PLIP MPD.30: 3 residues within 4Å: Chain D: P.353, E.355, E.356 Ligand excluded by PLIP MPD.35: 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.36: 5 residues within 4Å: Chain E: R.151, Y.152, Y.171, L.500 Ligands: MPD.42 Ligand excluded by PLIP MPD.37: 3 residues within 4Å: Chain E: E.308, V.312, D.359 Ligand excluded by PLIP MPD.42: 6 residues within 4Å: Chain F: R.151, Y.152, A.156, Y.171, L.500 Ligands: MPD.36 Ligand excluded by PLIP MPD.43: 7 residues within 4Å: Chain E: E.158, V.160 Chain F: F.6, Y.144, R.147, A.148, L.500 Ligand excluded by PLIP MPD.44: 6 residues within 4Å: Chain E: P.442, L.490 Chain F: L.275, G.278, Q.279, T.280 Ligand excluded by PLIP MPD.45: 3 residues within 4Å: Chain F: P.353, E.355, E.356 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inagaki, E. et al., New insights into the binding mode of coenzymes: structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase complexed with NADP+. Acta Crystallogr.,Sect.F (2007)

Release Date

2007-05-01

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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