SMTL ID : 3g1u.1

Crystal structure of Leishmania major S-adenosylhomocysteine hydrolase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x ADN: ADENOSINE(Non-covalent)

ADN.1: 18 residues within 4Å: Chain A: L.51, H.52, T.54, Q.56, T.57, D.130, E.155, T.156, N.190, H.300, L.343, L.346, S.350, G.351, H.352, M.357, F.361 Ligands: NAD.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.56, A:D.130, A:E.155, A:T.156, A:N.190, A:H.300, A:H.352 Water bridges: A:N.190 ADN.3: 17 residues within 4Å: Chain B: L.51, H.52, T.54, Q.56, T.57, D.130, E.155, T.156, H.300, L.343, L.346, S.350, G.351, H.352, M.357, F.361 Ligands: NAD.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.56, B:T.57, B:T.156, B:T.156, B:H.300, B:H.352 Water bridges: B:E.155, B:N.190, B:N.190 ADN.5: 19 residues within 4Å: Chain C: L.51, H.52, T.54, Q.56, T.57, D.130, E.155, T.156, K.185, D.189, H.300, L.343, L.346, S.350, G.351, H.352, M.357, F.361 Ligands: NAD.6 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.54, C:Q.56, C:T.57, C:T.156, C:T.156, C:K.185, C:D.189, C:H.300, C:H.352 Water bridges: C:Q.56 ADN.7: 18 residues within 4Å: Chain D: L.51, H.52, T.54, Q.56, T.57, D.130, E.155, T.156, D.189, H.300, L.343, L.346, S.350, G.351, H.352, M.357, F.361 Ligands: NAD.8 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.56, D:E.155, D:T.156, D:T.156, D:D.189, D:H.300, D:H.352

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

NAD.2: 28 residues within 4Å: Chain A: T.156, T.157, T.158, N.190, G.219, G.221, D.222, V.223, T.241, E.242, V.243, D.244, N.247, T.274, T.275, G.276, N.277, I.280, I.298, G.299, H.300, L.343, N.345, H.352 Chain D: L.414, Q.418, I.422 Ligands: ADN.1 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:N.190, A:V.223 Hydrogen bonds: A:T.158, A:G.221, A:V.223, A:T.241, A:V.243, A:D.244, A:H.300, A:N.345, A:N.345, D:Q.418, D:Q.418 Water bridges: A:T.157, A:D.222, A:D.222, A:G.224, A:N.247, D:T.412 NAD.4: 31 residues within 4Å: Chain B: T.156, T.157, T.158, K.161, N.190, G.219, Y.220, G.221, D.222, V.223, T.241, E.242, V.243, D.244, N.247, T.274, T.275, G.276, N.277, I.280, I.298, G.299, H.300, L.343, N.345, H.352 Chain C: L.414, Q.418, I.422, K.431 Ligands: ADN.3 23 PLIP interactions: 18 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:N.190, B:V.223 Hydrogen bonds: B:T.157, B:T.158, B:N.190, B:G.221, B:V.223, B:V.243, B:D.244, B:N.277, B:H.300, B:N.345, B:N.345, C:Q.418, C:Q.418, C:K.431, C:K.431 Water bridges: B:D.222, B:D.222, B:G.224, B:T.241 Salt bridges: B:K.161, C:K.431 NAD.6: 27 residues within 4Å: Chain B: Q.418 Chain C: T.156, T.157, T.158, D.189, N.190, G.219, G.221, D.222, V.223, T.241, E.242, V.243, D.244, N.247, T.274, T.275, G.276, N.277, I.280, I.298, G.299, H.300, L.343, N.345, H.352 Ligands: ADN.5 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:V.223 Hydrogen bonds: C:T.157, C:T.157, C:T.158, C:N.190, C:G.221, C:V.223, C:V.243, C:D.244, C:H.300, C:N.345, C:N.345 Water bridges: C:G.224, C:T.241, B:Q.418, B:Q.418 NAD.8: 30 residues within 4Å: Chain A: L.414, Q.418 Chain D: T.156, T.157, T.158, K.161, D.189, N.190, G.219, Y.220, G.221, D.222, V.223, T.241, E.242, V.243, D.244, N.247, T.274, T.275, G.276, N.277, I.280, I.298, G.299, H.300, L.343, N.345, H.352 Ligands: ADN.7 22 PLIP interactions: 20 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:N.190, D:V.223 Hydrogen bonds: D:T.157, D:T.158, D:T.158, D:N.190, D:G.221, D:V.223, D:V.243, D:D.244, D:N.277, D:I.298, D:H.300, D:N.345, A:Q.418, A:Q.418 Water bridges: D:D.222, D:D.222, D:G.224, D:N.247, D:T.274 Salt bridges: D:K.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Siponen, M.I. et al., Crystal structure of Leishmania major S-adenosylhomocysteine hydrolase. To be Published

Release Date

2009-02-10

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosylhomocysteinase