SMTL ID : 1c1d.1

L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 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.11 K.2: 6 residues within 4Å: Chain A: V.136, F.137, G.138, R.139, G.145, E.299 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.136, A:E.299 K.5: 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.22, H2O.26 K.6: 2 residues within 4Å: Chain B: D.118, T.121 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.121, H2O.24, H2O.27, H2O.31, H2O.32

2 x PHE: PHENYLALANINE(Non-covalent)

PHE.3: 13 residues within 4Å: Chain A: G.39, G.40, M.63, K.66, M.67, K.78, G.116, P.117, D.118, N.262, A.292, L.295 Ligands: NAI.4 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:A.292, A:L.295 Hydrogen bonds: A:P.117, A:D.118, A:N.262 Water bridges: A:K.66, A:K.66, A:K.78 Salt bridges: A:K.66, A:K.78 PHE.10: 12 residues within 4Å: Chain B: G.39, G.40, M.63, K.66, K.78, G.116, P.117, D.118, N.262, A.292, L.295 Ligands: NAI.11 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:A.292, B:L.295 Hydrogen bonds: B:K.78, B:D.118, B:D.118, B:D.118, B:N.262 Water bridges: B:K.66 Salt bridges: B:K.66, B:K.78

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.4: 24 residues within 4Å: Chain A: R.42, K.66, 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, L.224, C.238, A.239, A.260, A.261, N.262, N.288, G.291 Ligands: PHE.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.153, A:N.288 Hydrogen bonds: A:R.42, A:D.118, A:T.153, A:L.183, A:L.183, A:A.185, A:V.186, A:T.206, A:A.239, A:N.262, A:N.262 Water bridges: A:D.118, A:Q.181, A:G.184, A:G.187, A:G.241 NAI.11: 23 residues within 4Å: Chain B: R.42, D.118, 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: PHE.10 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.153, B:N.288 Hydrogen bonds: B:R.42, B:D.118, B:T.153, B:L.183, B:L.183, B:A.185, B:V.186, B:T.206, B:R.210, B:A.239, B:N.262, B:N.262 Water bridges: B:Q.181, B:G.184, B:G.187, B:T.206, B:T.206

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

NA.7: 2 residues within 4Å: Chain B: D.9, D.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.9, B:E.11 NA.8: 3 residues within 4Å: Chain B: Q.200, L.201, H.219 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.201, B:L.201 Water bridges: B:Q.200

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

PO4.9: 4 residues within 4Å: Chain B: S.1, S.4, T.54, K.58 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.1, B:S.1, B:S.1, B:S.4 Water bridges: B:S.4, B:T.54 Salt bridges: B:K.58

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

IPA.12: 6 residues within 4Å: Chain A: T.15, L.49 Chain B: A.5, L.6, T.13, R.28 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.49, B:L.6 Hydrogen bonds: A:T.15, B:A.5, B:T.13, B:R.28

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
L-PHENYLALANINE DEHYDROGENASE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

L-PHENYLALANINE DEHYDROGENASE

L-PHENYLALANINE DEHYDROGENASE