SMTL ID : 5axb.1

Crystal structure of mouse SAHH complexed with noraristeromycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 31 residues within 4Å: Chain A: T.157, T.158, T.159, D.190, N.191, C.195, G.220, G.222, D.223, V.224, T.242, E.243, I.244, D.245, N.248, T.275, T.276, G.277, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Chain C: L.409, Q.413, K.426, Y.430 Ligands: NRN.2 27 PLIP interactions: 21 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:V.224 Hydrogen bonds: A:T.158, A:T.158, A:T.158, A:T.159, A:T.159, A:D.223, A:V.224, A:T.242, A:I.244, A:D.245, A:N.248, A:H.301, A:N.346, A:N.346, C:Q.413, C:K.426, C:K.426, C:Y.430, C:Y.430 Water bridges: A:T.158, A:T.159, A:G.222, A:D.223, A:G.225, A:F.302, C:Q.413 NAD.4: 30 residues within 4Å: Chain B: T.157, T.158, T.159, D.190, N.191, C.195, G.220, G.222, D.223, V.224, T.242, E.243, I.244, D.245, N.248, T.275, T.276, G.277, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Chain D: Q.413, K.426, Y.430 Ligands: NRN.5 27 PLIP interactions: 22 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:V.224 Hydrogen bonds: B:T.158, B:T.158, B:T.158, B:T.159, B:D.223, B:V.224, B:I.244, B:D.245, B:N.248, B:I.299, B:H.301, B:N.346, D:Q.413, D:K.426, D:K.426, D:Y.430 Water bridges: B:T.159, B:G.222, B:D.223, B:D.223, B:G.225, B:T.242, B:G.300, B:F.302, B:E.305, D:Q.413 NAD.7: 31 residues within 4Å: Chain A: L.409, Q.413, K.426, Y.430 Chain C: T.157, T.158, T.159, D.190, N.191, C.195, G.220, G.222, D.223, V.224, T.242, E.243, I.244, D.245, N.248, T.275, T.276, G.277, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Ligands: NRN.8 27 PLIP interactions: 21 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:V.224 Hydrogen bonds: C:T.158, C:T.158, C:T.158, C:T.159, C:T.159, C:D.223, C:V.224, C:T.242, C:I.244, C:D.245, C:N.248, C:H.301, C:N.346, C:N.346, A:Q.413, A:K.426, A:K.426, A:Y.430, A:Y.430 Water bridges: C:T.158, C:T.159, C:G.222, C:D.223, C:G.225, C:F.302, A:Q.413 NAD.10: 30 residues within 4Å: Chain B: Q.413, K.426, Y.430 Chain D: T.157, T.158, T.159, D.190, N.191, C.195, G.220, G.222, D.223, V.224, T.242, E.243, I.244, D.245, N.248, T.275, T.276, G.277, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Ligands: NRN.11 27 PLIP interactions: 22 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:V.224 Hydrogen bonds: D:T.158, D:T.158, D:T.158, D:T.159, D:D.223, D:V.224, D:I.244, D:D.245, D:N.248, D:I.299, D:H.301, D:N.346, B:Q.413, B:K.426, B:K.426, B:Y.430 Water bridges: D:T.159, D:G.222, D:D.223, D:D.223, D:G.225, D:T.242, D:G.300, D:F.302, D:E.305, B:Q.413

4 x NRN: (1S,2R,3S,4R)-4-(6-aminopurin-9-yl)cyclopentane-1,2,3-triol(Non-covalent)

NRN.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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.347 Hydrogen bonds: A:E.59, A:D.131, A:E.156, A:T.157, A:K.186, A:K.186, A:H.353 NRN.5: 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.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.347 Hydrogen bonds: B:T.57, B:E.59, B:E.59, B:T.60, B:D.131, B:T.157, B:K.186, B:K.186, B:H.353 NRN.8: 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.7 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.347 Hydrogen bonds: C:E.59, C:D.131, C:E.156, C:T.157, C:K.186, C:K.186, C:H.353 NRN.11: 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.10 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.347 Hydrogen bonds: D:T.57, D:E.59, D:E.59, D:T.60, D:D.131, D:T.157, D:K.186, D:K.186, D:H.353

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

NA.3: 2 residues within 4Å: Chain A: E.59 Chain B: D.208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.59 NA.6: 2 residues within 4Å: Chain A: D.208 Chain B: E.59 No protein-ligand interaction detected (PLIP) NA.9: 2 residues within 4Å: Chain C: E.59 Chain D: D.208 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.59 NA.12: 2 residues within 4Å: Chain C: D.208 Chain D: E.59 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kusakabe, Y. et al., Crystal structure of mouse SAHH complexed with noraristeromycin. To Be Published

Release Date

2016-07-27

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

Adenosylhomocysteinase

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