SMTL ID : 1bw9.1

PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND PHENYLPYRUVATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: K.67, K.79, P.118, D.119, V.120, G.183, L.184, G.185, A.186, V.187, G.188, A.205, D.206, T.207, R.211, L.225, C.239, A.240, M.241, A.261, A.262, N.263 Ligands: PPY.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:D.119 Hydrogen bonds: A:K.79, A:D.119, A:L.184, A:L.184, A:A.186, A:V.187, A:G.188, A:T.207, A:T.207, A:A.240, A:N.263, A:N.263, A:N.263 Water bridges: A:R.43, A:S.150, A:Q.182, A:G.185, A:R.211, A:R.211, A:G.242 NAD.8: 13 residues within 4Å: Chain B: G.183, L.184, G.185, A.186, V.187, A.205, D.206, T.207, D.208, R.211, L.225, A.240, M.241 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:L.184, B:L.184, B:A.186, B:V.187, B:T.207, B:T.207, B:D.208, B:R.211 Water bridges: B:N.121, B:Q.182, B:G.185, B:G.188, B:T.207

2 x PPY: 3-PHENYLPYRUVIC ACID(Non-covalent)

PPY.2: 15 residues within 4Å: Chain A: A.39, G.40, G.41, M.64, K.67, M.68, K.79, T.116, G.117, P.118, F.138, G.292, A.293, L.296 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.39, A:F.138, A:A.293, A:L.296 Hydrogen bonds: A:G.41 Water bridges: A:K.67, A:A.293 Salt bridges: A:K.67, A:K.79 PPY.9: 15 residues within 4Å: Chain B: A.39, G.40, G.41, M.64, K.67, M.68, K.79, T.116, G.117, P.118, D.119, F.138, N.263, A.293, L.296 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.39, B:F.138, B:A.293, B:L.296 Hydrogen bonds: B:G.41, B:D.119, B:D.119, B:N.263, B:A.293 Water bridges: B:K.67 Salt bridges: B:K.67, B:K.79

2 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.6: 4 residues within 4Å: Chain B: L.171, S.173, D.175, L.177 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.173, B:D.175, H2O.25, H2O.30

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

NA.4: 1 residues within 4Å: Chain B: D.10 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.10 Water bridges: A:R.17 NA.5: 2 residues within 4Å: Chain B: Q.201, G.219 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.201 Water bridges: B:L.202, B:G.219, B:T.221

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 4 residues within 4Å: Chain B: S.2, S.5, T.55, K.59 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.2, B:S.2, B:S.2, B:S.5 Water bridges: B:K.59, B:K.59, B:K.59 Salt bridges: B:K.59

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) IPA.14: 5 residues within 4Å: Chain B: L.35, G.36, P.37, P.74, V.301 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.301 IPA.15: 8 residues within 4Å: Chain B: R.43, D.56, K.59, L.60, G.242, G.243, N.263, N.264 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.59, B:N.264 Hydrogen bonds: B:R.43, B:N.264 Water bridges: B:G.242, B:G.242 IPA.16: 7 residues within 4Å: Chain A: T.16, L.50 Chain B: A.6, L.7, T.14, R.29, L.54 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.50, B:L.7, B:L.54 Hydrogen bonds: A:T.16, B:T.14, B:R.29 Water bridges: A:T.16, B:T.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vanhooke, J.L. et al., Phenylalanine dehydrogenase from Rhodococcus sp. M4: high-resolution X-ray analyses of inhibitory ternary complexes reveal key features in the oxidative deamination mechanism. Biochemistry (1999)

Release Date

1999-05-18

Peptides

PHENYLALANINE DEHYDROGENASE: A
PHENYLALANINE DEHYDROGENASE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PHENYLALANINE DEHYDROGENASE

PHENYLALANINE DEHYDROGENASE