SMTL ID : 3n58.1

Crystal structure of S-ADENOSYL-L-HOMOCYSTEINE hydrolase from brucella melitensis in ternary complex with NAD and adenosine, orthorhombic form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-tetramer

Ligands

3 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: Q.57, T.383, G.384, H.385 Ligands: ADN.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.383 K.5: 5 residues within 4Å: Chain C: Q.57, T.383, G.384, H.385 Ligands: ADN.6 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.383, H2O.16 K.8: 5 residues within 4Å: Chain D: Q.57, T.383, G.384, H.385, P.386 No protein-ligand interaction detected (PLIP)

3 x ADN: ADENOSINE(Non-covalent)

ADN.2: 20 residues within 4Å: Chain A: L.52, H.53, T.55, Q.57, T.58, D.130, E.190, T.191, K.220, D.224, H.335, L.376, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: K.1, NAD.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.55, A:Q.57, A:E.190, A:T.191, A:T.191, A:K.220, A:K.220, A:H.335, A:H.385 ADN.6: 20 residues within 4Å: Chain C: L.52, H.53, T.55, Q.57, T.58, D.130, E.190, T.191, K.220, D.224, H.335, L.376, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: K.5, NAD.7 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.57, C:T.58, C:T.191, C:K.220, C:K.220, C:H.335, C:H.385 ADN.9: 19 residues within 4Å: Chain D: L.52, H.53, T.55, Q.57, T.58, D.130, E.190, T.191, K.220, D.224, H.335, L.376, L.379, T.383, G.384, H.385, M.390, F.394 Ligands: NAD.10 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.55, D:Q.57, D:T.58, D:T.191, D:T.191, D:K.220, D:K.220, D:H.385

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

NAD.3: 29 residues within 4Å: Chain A: T.191, T.192, T.193, D.224, N.225, G.254, G.256, D.257, V.258, T.276, E.277, V.278, D.279, C.282, T.309, T.310, G.311, N.312, I.333, G.334, H.335, L.376, N.378, H.385 Chain B: L.441, Q.445, K.458, Y.462 Ligands: ADN.2 25 PLIP interactions: 19 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.258 Hydrogen bonds: A:T.193, A:T.193, A:N.225, A:G.256, A:D.257, A:V.258, A:T.276, A:V.278, A:D.279, A:N.312, A:H.335, A:N.378, A:N.378, B:Q.445, B:K.458, B:K.458, B:Y.462, B:Y.462 Water bridges: A:T.192, A:N.215, A:G.259, A:G.311, A:F.336, B:Q.445 NAD.4: 26 residues within 4Å: Chain A: L.441, Q.445, K.458, Y.462 Chain B: D.224, N.225, C.229, G.254, G.256, D.257, V.258, T.276, E.277, V.278, D.279, C.282, T.309, T.310, G.311, N.312, I.333, G.334, H.335, L.376, N.378, H.385 19 PLIP interactions: 13 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:V.258 Hydrogen bonds: B:G.256, B:D.257, B:V.258, B:T.276, B:V.278, B:D.279, B:N.312, B:N.378, B:N.378, A:K.458, A:K.458, A:Y.462, A:Y.462 Water bridges: B:N.225, B:N.225, B:G.259, A:Q.445, A:Q.445 NAD.7: 29 residues within 4Å: Chain C: T.191, T.192, T.193, D.224, N.225, G.254, G.256, D.257, V.258, T.276, E.277, V.278, D.279, C.282, T.309, T.310, G.311, N.312, I.333, G.334, H.335, L.376, N.378, H.385 Chain D: L.441, Q.445, K.458, Y.462 Ligands: ADN.6 24 PLIP interactions: 18 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:V.258 Hydrogen bonds: C:T.193, C:T.193, C:N.225, C:D.257, C:V.258, C:T.276, C:V.278, C:N.312, C:H.335, C:N.378, C:N.378, D:K.458, D:K.458, D:Y.462 Water bridges: C:N.215, C:G.256, C:D.257, C:G.259, C:G.311, C:F.336, D:T.439, D:Q.445, D:Q.445 NAD.10: 30 residues within 4Å: Chain C: L.441, Q.445, K.458, Y.462 Chain D: T.191, T.192, T.193, D.224, N.225, G.254, G.256, D.257, V.258, T.276, E.277, V.278, D.279, C.282, T.309, T.310, G.311, N.312, V.315, I.333, G.334, H.335, L.376, N.378, H.385 Ligands: ADN.9 23 PLIP interactions: 18 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:V.258 Hydrogen bonds: D:T.192, D:T.192, D:T.193, D:N.225, D:G.256, D:D.257, D:V.258, D:V.278, D:D.279, D:N.312, D:H.335, D:N.378, D:N.378, C:K.458, C:K.458, C:Y.462 Water bridges: D:T.193, D:G.259, D:T.276, D:F.336, C:Q.445, C:Q.445

Links

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Citation

SSGCID et al., Crystal structure of S-adenosyl-L-homocysteine hydrolase from brucella melitensis in ternary complex with NAD and adenosine, orthorhombic form. To be Published

Release Date

2010-06-02

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosylhomocysteinase