SMTL ID : 1a7a.1

STRUCTURE OF HUMAN PLACENTAL S-ADENOSYLHOMOCYSTEINE HYDROLASE: DETERMINATION OF A 30 SELENIUM ATOM SUBSTRUCTURE FROM DATA AT A SINGLE WAVELENGTH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 29 residues within 4Å: Chain A: T.157, T.158, T.159, D.190, N.191, G.220, G.222, D.223, V.224, T.242, E.243, I.244, D.245, N.248, T.275, T.276, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Chain B: Q.413, L.417, K.426, Y.430 Ligands: ADC.2 22 PLIP interactions: 16 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.224 Hydrogen bonds: A:T.158, A:T.158, A:T.158, A:T.159, A:T.159, A:T.159, A:D.223, A:V.224, A:I.244, A:T.276, A:I.299, A:H.301, A:N.346, B:Q.413, B:K.426, B:K.426, B:Y.430, B:Y.430 Water bridges: A:G.222, A:G.222 Salt bridges: B:K.426 NAD.3: 30 residues within 4Å: Chain A: L.409, Q.413, L.417, K.426, Y.430 Chain B: T.157, T.158, T.159, D.190, N.191, G.220, G.222, D.223, V.224, T.242, E.243, I.244, D.245, N.248, T.275, T.276, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Ligands: ADC.4 21 PLIP interactions: 6 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:Q.413, A:K.426, A:K.426, A:Y.430, A:Y.430, B:T.158, B:T.158, B:T.159, B:T.159, B:D.223, B:V.224, B:I.244, B:T.276, B:T.276, B:I.299, B:H.301, B:N.346 Salt bridges: A:K.426 Hydrophobic interactions: B:V.224 Water bridges: B:G.222, B:G.225 NAD.5: 29 residues within 4Å: Chain C: T.157, T.158, T.159, D.190, N.191, G.220, G.222, D.223, V.224, T.242, E.243, I.244, D.245, N.248, T.275, T.276, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Chain D: Q.413, L.417, K.426, Y.430 Ligands: ADC.6 22 PLIP interactions: 16 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:V.224 Hydrogen bonds: C:T.158, C:T.158, C:T.158, C:T.159, C:T.159, C:T.159, C:D.223, C:V.224, C:I.244, C:T.276, C:I.299, C:H.301, C:N.346, D:Q.413, D:K.426, D:K.426, D:Y.430, D:Y.430 Water bridges: C:G.222, C:G.222 Salt bridges: D:K.426 NAD.7: 30 residues within 4Å: Chain C: L.409, Q.413, L.417, K.426, Y.430 Chain D: T.157, T.158, T.159, D.190, N.191, G.220, G.222, D.223, V.224, T.242, E.243, I.244, D.245, N.248, T.275, T.276, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Ligands: ADC.8 21 PLIP interactions: 15 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:V.224 Hydrogen bonds: D:T.158, D:T.158, D:T.159, D:T.159, D:D.223, D:V.224, D:I.244, D:T.276, D:T.276, D:I.299, D:H.301, D:N.346, C:Q.413, C:K.426, C:K.426, C:Y.430, C:Y.430 Water bridges: D:G.222, D:G.225 Salt bridges: C:K.426

4 x ADC: (1'R,2'S)-9-(2-HYDROXY-3'-KETO-CYCLOPENTEN-1-YL)ADENINE(Non-covalent)

ADC.2: 17 residues within 4Å: Chain A: L.54, H.55, T.57, E.59, T.60, D.131, E.156, T.157, K.186, D.190, L.347, M.351, G.352, H.353, M.358, F.362 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.347 Hydrogen bonds: A:T.57, A:E.59, A:E.59, A:T.60, A:T.157, A:K.186, A:D.190, A:H.353 ADC.4: 17 residues within 4Å: Chain B: L.54, H.55, T.57, E.59, T.60, D.131, E.156, T.157, K.186, D.190, L.347, M.351, G.352, H.353, M.358, F.362 Ligands: NAD.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.347 Hydrogen bonds: B:E.59, B:K.186, B:D.190, B:H.353 ADC.6: 17 residues within 4Å: Chain C: L.54, H.55, T.57, E.59, T.60, D.131, E.156, T.157, K.186, D.190, L.347, M.351, G.352, H.353, M.358, F.362 Ligands: NAD.5 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.347 Hydrogen bonds: C:T.57, C:E.59, C:E.59, C:T.60, C:T.157, C:K.186, C:D.190, C:H.353 ADC.8: 17 residues within 4Å: Chain D: L.54, H.55, T.57, E.59, T.60, D.131, E.156, T.157, K.186, D.190, L.347, M.351, G.352, H.353, M.358, F.362 Ligands: NAD.7 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.347 Hydrogen bonds: D:E.59, D:K.186, D:D.190, D:H.353

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Turner, M.A. et al., Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength. Nat.Struct.Biol. (1998)

Release Date

1999-04-20

Peptides

S-ADENOSYLHOMOCYSTEINE HYDROLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

S-ADENOSYLHOMOCYSTEINE HYDROLASE