SMTL ID : 1c1x.1

L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND L-3-PHENYLLACTATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 2 residues within 4Å: Chain A: D.118, T.121 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.118, A:T.121, H2O.9, H2O.10 K.2: 5 residues within 4Å: Chain A: W.8, D.9, G.10 Chain B: R.16, F.17 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:W.8, A:G.10, H2O.15 K.6: 4 residues within 4Å: Chain B: L.170, S.172, D.174, L.176 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.172, B:D.174, H2O.20, H2O.25 K.7: 2 residues within 4Å: Chain B: D.118, T.121 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.118, B:T.121, H2O.27, H2O.29

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

NA.3: 6 residues within 4Å: Chain A: R.87, W.95, N.120, T.121, N.122, D.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.87, A:D.125 Water bridges: A:N.122

2 x HFA: ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC ACID(Non-covalent)

HFA.4: 15 residues within 4Å: Chain A: A.38, G.39, G.40, M.63, K.66, M.67, K.78, T.115, G.116, P.117, F.137, G.291, A.292, L.295 Ligands: NAD.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.38, A:F.137, A:A.292, A:L.295 Hydrogen bonds: A:G.40, A:K.78 Water bridges: A:K.66, A:G.291 Salt bridges: A:K.66, A:K.78 HFA.10: 14 residues within 4Å: Chain B: A.38, G.39, G.40, M.63, K.66, M.67, K.78, G.116, P.117, F.137, G.291, A.292, L.295 Ligands: NAD.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.38, B:F.137, B:A.292, B:L.295 Hydrogen bonds: B:G.40, B:K.78, B:D.118 Water bridges: B:K.66, B:G.291 Salt bridges: B:K.66, B:K.78

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

NAD.5: 23 residues within 4Å: Chain A: D.118, V.119, S.149, A.150, T.153, G.182, L.183, G.184, A.185, V.186, A.204, D.205, T.206, R.210, L.224, C.238, A.239, M.240, A.260, A.261, N.262, N.288 Ligands: HFA.4 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:T.153 Hydrogen bonds: A:D.118, A:T.153, A:L.183, A:L.183, A:A.185, A:V.186, A:T.206, A:T.206, A:A.239, A:N.262, A:N.262 Water bridges: A:D.118, A:D.118, A:S.149, A:G.184, A:G.187, A:R.210, A:R.210, A:R.210, A:G.241 NAD.9: 23 residues within 4Å: Chain B: R.42, D.118, S.149, T.153, Q.181, G.182, L.183, G.184, A.185, V.186, A.204, D.205, T.206, R.210, L.224, C.238, A.239, M.240, A.260, A.261, N.262, N.288 Ligands: HFA.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:T.153 Hydrogen bonds: B:R.42, B:T.153, B:L.183, B:A.185, B:V.186, B:T.206, B:T.206, B:R.210, B:R.210, B:A.239, B:N.262, B:N.262 Water bridges: B:S.149, B:Q.181, B:G.184, B:G.187, B:G.241

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

PO4.8: 4 residues within 4Å: Chain B: S.1, S.4, T.54, K.58 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.1, B:S.1, B:S.1, B:S.4 Water bridges: B:T.54, B:K.58, B:K.58, B:K.58, B:K.58, B:K.58 Salt bridges: B:K.58

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

IPA.11: 5 residues within 4Å: Chain B: L.34, G.35, P.36, P.73, V.300 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.300 IPA.12: 6 residues within 4Å: Chain A: T.15, L.49 Chain B: L.6, T.13, R.28, L.53 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.6, B:L.53, A:L.49 Hydrogen bonds: B:T.13, B:R.28, A:T.15 Water bridges: B:T.13, A:T.15 IPA.13: 5 residues within 4Å: Chain B: Y.46, S.47, Q.48, L.49, A.82 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.49, B:A.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brunhuber, N.M. et al., Rhodococcus L-phenylalanine dehydrogenase: kinetics, mechanism, and structural basis for catalytic specificity. Biochemistry (2000)

Release Date

2000-08-30

Peptides

L-PHENYLALANINE DEHYDROGENASE: A
PROTEIN (L-PHENYLALANINE DEHYDROGENASE): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

L-PHENYLALANINE DEHYDROGENASE

PROTEIN (L-PHENYLALANINE DEHYDROGENASE)