SMTL ID : 1v8b.1

Crystal structure of a hydrolase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: T.201, T.202, T.203, D.234, N.235, C.239, G.264, G.266, D.267, V.268, T.286, E.287, I.288, D.289, C.292, C.319, T.320, G.321, N.322, V.325, I.343, G.344, H.345, L.389, N.391, H.398 Chain B: Q.460, K.473, Y.477 Ligands: ADN.2 24 PLIP interactions: 18 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.268 Hydrogen bonds: A:T.202, A:T.202, A:T.202, A:T.203, A:T.203, A:D.267, A:D.267, A:V.268, A:I.288, A:D.289, A:N.322, A:I.343, A:N.391, B:Q.460, B:K.473, B:K.473, B:Y.477 Water bridges: A:T.202, A:G.266, A:D.267, A:G.269, B:Q.460, B:Q.460 NAD.3: 30 residues within 4Å: Chain A: Q.460, K.473, Y.477 Chain B: T.201, T.202, T.203, D.234, N.235, G.264, Y.265, G.266, D.267, V.268, T.286, E.287, I.288, D.289, C.292, C.319, T.320, G.321, N.322, V.325, I.343, G.344, H.345, L.389, N.391, H.398 Ligands: ADN.4 21 PLIP interactions: 6 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:Q.460, A:Q.460, A:K.473, A:K.473, A:Y.477, A:Y.477, B:T.202, B:T.203, B:T.203, B:Y.265, B:D.267, B:V.268, B:I.288, B:D.289, B:N.322, B:I.343, B:N.391 Hydrophobic interactions: B:V.268 Water bridges: B:G.266, B:G.269, B:T.286 NAD.5: 30 residues within 4Å: Chain C: T.201, T.202, T.203, D.234, N.235, G.264, Y.265, G.266, D.267, V.268, T.286, E.287, I.288, D.289, C.292, C.319, T.320, G.321, N.322, V.325, I.343, G.344, H.345, L.389, N.391, H.398 Chain D: Q.460, K.473, Y.477 Ligands: ADN.6 26 PLIP interactions: 21 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:V.268 Hydrogen bonds: C:T.202, C:T.202, C:T.203, C:T.203, C:T.203, C:Y.265, C:Y.265, C:D.267, C:D.267, C:V.268, C:T.286, C:I.288, C:D.289, C:N.322, C:I.343, C:N.391, D:Q.460, D:K.473, D:K.473, D:Y.477 Water bridges: C:T.202, C:G.266, C:D.267, C:G.269, D:Q.460 NAD.7: 31 residues within 4Å: Chain C: Q.460, K.473, Y.477 Chain D: T.201, T.202, T.203, D.234, N.235, C.239, G.264, Y.265, G.266, D.267, V.268, T.286, E.287, I.288, D.289, C.292, C.319, T.320, G.321, N.322, V.325, I.343, G.344, H.345, L.389, N.391, H.398 Ligands: ADN.8 19 PLIP interactions: 6 interactions with chain C, 13 interactions with chain D Hydrogen bonds: C:Q.460, C:K.473, C:K.473, C:Y.477, C:Y.477, D:T.202, D:T.203, D:T.203, D:D.267, D:V.268, D:I.288, D:D.289, D:N.322, D:I.343, D:N.391 Water bridges: C:Q.460, D:G.266, D:G.269 Hydrophobic interactions: D:V.268

4 x ADN: ADENOSINE(Non-covalent)

ADN.2: 17 residues within 4Å: Chain A: L.53, H.54, T.56, E.58, D.134, E.200, T.201, K.230, D.234, L.389, L.392, T.396, G.397, H.398, M.403, F.407 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.56, A:E.58, A:E.58, A:T.201, A:T.201, A:K.230, A:K.230, A:H.398 ADN.4: 17 residues within 4Å: Chain B: L.53, H.54, T.56, E.58, D.134, E.200, T.201, K.230, D.234, L.389, L.392, T.396, G.397, H.398, M.403, F.407 Ligands: NAD.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.58, B:E.200, B:T.201, B:K.230, B:K.230, B:H.398 Water bridges: B:D.134, B:D.134 ADN.6: 17 residues within 4Å: Chain C: L.53, H.54, T.56, E.58, D.134, E.200, T.201, K.230, D.234, L.389, L.392, T.396, G.397, H.398, M.403, F.407 Ligands: NAD.5 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.56, C:E.58, C:E.58, C:T.201, C:T.201, C:K.230, C:K.230, C:H.398 ADN.8: 17 residues within 4Å: Chain D: L.53, H.54, T.56, E.58, D.134, E.200, T.201, K.230, D.234, L.389, L.392, T.396, G.397, H.398, M.403, F.407 Ligands: NAD.7 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.58, D:E.200, D:T.201, D:K.230, D:K.230, D:H.398

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, N. et al., Crystal Structure of S-Adenosyl-l-Homocysteine Hydrolase from the Human Malaria Parasite Plasmodium falciparum. J.Mol.Biol. (2004)

Release Date

2004-10-26

Peptides

adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

adenosylhomocysteinase