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

Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound L-alanine and NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

4 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: NAD.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.248, 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.11: 7 residues within 4Å: Chain B: A.245, V.248, E.249, K.267, I.268, A.271 Ligands: NAD.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.248, B:A.271 ACT.12: 6 residues within 4Å: Chain A: V.172, K.510 Chain B: R.461, R.462, F.464, H.465 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Water bridges: B:R.462, B:H.465 Salt bridges: B:H.465, A:K.510 Hydrophobic interactions: A:V.172, A:K.510

2 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:E.123 NA.13: 4 residues within 4Å: Chain B: S.55, L.56, E.123, D.211 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.56, B:E.123 Water bridges: B:D.211, B:D.211

2 x ALA: ALANINE(Non-covalent)

ALA.4: 7 residues within 4Å: Chain A: F.185, C.322, S.323, T.476, G.477, A.478, F.485 10 PLIP interactions: 8 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.185, A:F.485 Hydrogen bonds: A:S.323, A:G.477, A:A.478 Water bridges: A:E.137, A:E.137, A:E.137, A.4, A.4 ALA.14: 7 residues within 4Å: Chain B: F.185, C.322, S.323, T.476, G.477, A.478, F.485 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.185, B:F.485 Hydrogen bonds: B:S.323, B:G.477, B:A.478 Water bridges: B:E.137, B:E.137, B:E.137, B:E.137, A.14

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

NAD.5: 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.1 12 PLIP interactions: 12 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:G.290, A:E.417 Water bridges: A:L.262 NAD.15: 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: ACT.11 15 PLIP interactions: 15 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:E.288, B:G.290, B:E.417

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

MPD.6: 6 residues within 4Å: Chain A: E.158 Chain B: F.6, Y.144, R.147, A.148, L.500 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.6, B:R.147, B:A.148, B:L.500 Hydrogen bonds: A:E.158 MPD.7: 4 residues within 4Å: Chain A: V.312, Y.315, G.316, D.359 No protein-ligand interaction detected (PLIP) MPD.8: 5 residues within 4Å: Chain A: R.151, Y.152, Y.171, L.500 Ligands: MPD.19 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.151, A:Y.152, A:L.500 Hydrogen bonds: A:R.151, A:Y.171, A:Y.171 MPD.9: 7 residues within 4Å: Chain A: F.6, Y.144, R.147, A.148, L.500 Chain B: E.158, V.160 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.6, A:Y.144, A:R.147, A:A.148, A:L.500, B:V.160 Hydrogen bonds: B:E.158 MPD.10: 5 residues within 4Å: Chain A: L.275, G.278, Q.279 Chain B: P.442, L.490 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.490, A:L.275 Hydrogen bonds: A:G.278 MPD.16: 5 residues within 4Å: Chain B: R.36, Y.38, P.39, W.46, E.221 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.38, B:W.46, B:W.46 Hydrogen bonds: B:R.36, B:E.221, B:E.221 MPD.17: 3 residues within 4Å: Chain B: P.353, E.355, E.356 No protein-ligand interaction detected (PLIP) MPD.18: 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 MPD.19: 6 residues within 4Å: Chain B: R.151, Y.152, A.156, Y.171, L.500 Ligands: MPD.8 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.151, B:Y.152, B:A.156, B:Y.171, B:L.500 Water bridges: B:Y.152, B:Y.171, A:D.501

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

1-pyrroline-5-carboxylate dehydrogenase

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