SMTL ID : 1li4.1

Human S-adenosylhomocysteine hydrolase complexed with neplanocin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 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, K.186, 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, G.277, 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: NOC.2 27 PLIP interactions: 22 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:N.191, A:V.224 Hydrogen bonds: A:T.158, A:T.159, A:T.159, A:D.223, A:V.224, A:I.244, A:D.245, A:N.248, A:I.299, A:H.301, A:N.346, B:Q.413, B:K.426, B:K.426, B:Y.430 Water bridges: A:T.159, A:G.222, A:D.223, A:D.223, A:G.225, A:T.242, A:G.300, A:F.302, A:E.305, B:Q.413 NAD.5: 31 residues within 4Å: Chain A: Q.413, L.417, K.426, Y.430 Chain B: T.157, T.158, T.159, K.186, 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, G.277, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Ligands: NOC.6 27 PLIP interactions: 22 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:N.191, B:V.224 Hydrogen bonds: B:T.158, B:T.159, 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, A:Q.413, A:K.426, A:K.426, A: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, A:Q.413 NAD.9: 31 residues within 4Å: Chain C: T.157, T.158, T.159, K.186, 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, G.277, 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: NOC.10 29 PLIP interactions: 7 interactions with chain D, 22 interactions with chain C Hydrogen bonds: D:Q.413, D:K.426, D:K.426, D:Y.430, D:Y.430, C:T.159, 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:I.299, C:H.301, C:N.346 Water bridges: D:T.407, D:Q.413, C:T.158, C:T.159, C:G.222, C:D.223, C:G.225, C:G.277, C:F.302, C:E.305 Hydrophobic interactions: C:N.191, C:V.224 NAD.13: 31 residues within 4Å: Chain C: Q.413, L.417, K.426, Y.430 Chain D: T.157, T.158, T.159, K.186, 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, G.277, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Ligands: NOC.14 29 PLIP interactions: 22 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:N.191, D:V.224 Hydrogen bonds: D:T.159, D:T.159, D:T.159, D:D.223, D:V.224, D:T.242, D:I.244, D:D.245, D:N.248, 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:T.158, D:T.159, D:G.222, D:D.223, D:G.225, D:G.277, D:F.302, D:E.305, C:T.407, C:Q.413

4 x NOC: 3-(6-AMINO-PURIN-9-YL)-5-HYDROXYMETHYL-CYCLOPENTANE-1,2-DIOL(Non-covalent)

NOC.2: 18 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, H.301, L.347, M.351, G.352, H.353, M.358, F.362 Ligands: NAD.1 10 PLIP interactions: 10 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:K.186, A:H.301, A:H.353 NOC.6: 18 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, H.301, L.347, M.351, G.352, H.353, M.358, F.362 Ligands: NAD.5 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:T.157, B:K.186, B:K.186, B:H.301, B:H.353 NOC.10: 18 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, H.301, L.347, M.351, G.352, H.353, M.358, F.362 Ligands: NAD.9 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.347 Hydrogen bonds: C:E.59, C:E.156, C:T.157, C:K.186, C:K.186, C:H.301, C:H.353 NOC.14: 18 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, H.301, L.347, M.351, G.352, H.353, M.358, F.362 Ligands: NAD.13 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.347 Hydrogen bonds: D:E.59, D:E.156, D:T.157, D:K.186, D:K.186, D:H.301, D:H.353

8 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 7 residues within 4Å: Chain A: R.238 Chain C: L.402, V.404 Chain D: A.253, Y.257, E.258, V.259 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: C:V.404, D:A.253 Hydrogen bonds: A:R.238 Water bridges: A:R.238 IPA.4: 6 residues within 4Å: Chain A: W.17, T.84, Q.85, D.86, H.87, M.351 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.17 Hydrogen bonds: A:T.84, A:D.86 IPA.7: 7 residues within 4Å: Chain B: R.238 Chain C: A.253, Y.257, E.258, V.259 Chain D: L.402, V.404 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: C:A.253, D:V.404 Hydrogen bonds: B:R.238 Water bridges: B:R.238 IPA.8: 6 residues within 4Å: Chain B: W.17, T.84, Q.85, D.86, H.87, M.351 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.17 Hydrogen bonds: B:T.84, B:D.86 IPA.11: 7 residues within 4Å: Chain A: L.402, V.404 Chain B: A.253, Y.257, E.258, V.259 Chain C: R.238 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: A:V.404, B:A.253 Hydrogen bonds: C:R.238 Water bridges: C:R.238 IPA.12: 6 residues within 4Å: Chain C: W.17, T.84, Q.85, D.86, H.87, M.351 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.17 Hydrogen bonds: C:T.84, C:D.86 IPA.15: 7 residues within 4Å: Chain A: A.253, Y.257, E.258, V.259 Chain B: L.402, V.404 Chain D: R.238 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:R.238 Water bridges: D:R.238 Hydrophobic interactions: B:V.404, A:A.253 IPA.16: 6 residues within 4Å: Chain D: W.17, T.84, Q.85, D.86, H.87, M.351 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.17 Hydrogen bonds: D:T.84, D:D.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X. et al., Catalytic strategy of S-adenosyl-L-homocysteine hydrolase: Transition-statestabilization and the avoidance of abortive reactions. Biochemistry (2003)

Release Date

2003-05-20

Peptides

S-adenosylhomocysteine hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

S-adenosylhomocysteine hydrolase

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