SMTL ID : 6uk3.1 (1 other biounit)

Crystal Structure of S-adenosyl-L-homocysteine hydrolase from Acanthamoeba castellanii with bound NAD and Adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: T.211, T.212, T.213, D.244, N.245, G.274, G.276, D.277, V.278, T.296, E.297, V.298, D.299, C.302, T.329, T.330, G.331, N.332, I.335, I.353, G.354, H.355, L.399, N.401, H.408 Chain B: L.462, Q.466, K.479, Y.483 Ligands: ADN.2 24 PLIP interactions: 18 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.278 Hydrogen bonds: A:T.212, A:T.212, A:T.212, A:T.213, A:T.213, A:N.245, A:G.276, A:D.277, A:V.278, A:T.296, A:V.298, A:D.299, A:N.332, A:N.401, A:N.401, B:Q.466, B:Q.466, B:K.479, B:K.479, B:Y.483 Water bridges: A:N.235, A:G.279, B:T.460 NAD.6: 29 residues within 4Å: Chain A: Q.466, K.479, Y.483 Chain B: T.211, T.212, T.213, D.244, N.245, G.274, G.276, D.277, V.278, T.296, E.297, V.298, D.299, C.302, T.329, T.330, G.331, N.332, I.335, I.353, G.354, H.355, L.399, N.401, H.408 Ligands: ADN.7 23 PLIP interactions: 17 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:V.278 Hydrogen bonds: B:T.212, B:T.212, B:T.212, B:T.213, B:N.245, B:G.276, B:D.277, B:V.278, B:T.296, B:V.298, B:D.299, B:N.332, B:N.401, B:N.401, A:Q.466, A:Q.466, A:K.479, A:K.479, A:Y.483 Water bridges: B:N.235, B:G.279, A:T.460

2 x ADN: ADENOSINE(Non-covalent)

ADN.2: 19 residues within 4Å: Chain A: L.71, H.72, T.74, Q.76, T.77, D.149, E.210, T.211, K.240, D.244, L.399, L.402, T.406, G.407, H.408, M.413, F.417 Ligands: NAD.1, K.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.76, A:E.210, A:T.211, A:T.211, A:K.240, A:K.240, A:H.408 ADN.7: 19 residues within 4Å: Chain B: L.71, H.72, T.74, Q.76, T.77, D.149, E.210, T.211, K.240, D.244, L.399, L.402, T.406, G.407, H.408, M.413, F.417 Ligands: NAD.6, K.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.74, B:Q.76, B:E.210, B:T.211, B:K.240, B:K.240, B:H.408

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 3 residues within 4Å: Chain A: H.346, N.347, Q.382 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.346, A:N.347, A:Q.382 FMT.8: 3 residues within 4Å: Chain B: H.346, N.347, Q.382 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.347, B:Q.382 Water bridges: B:Q.382 FMT.10: 1 residues within 4Å: Chain B: F.34 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: Q.76, T.406, G.407, H.408 Ligands: ADN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.406, A:T.406, A:H.408, H2O.11, H2O.13 K.11: 5 residues within 4Å: Chain B: Q.76, T.406, G.407, H.408 Ligands: ADN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.406, B:T.406, B:H.408, H2O.36, H2O.38

1 x OXM: OXAMIC ACID(Non-covalent)

OXM.5: 4 residues within 4Å: Chain A: L.155, S.176, E.178, R.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.176, A:E.178 Water bridges: A:R.217, A:R.217 Salt bridges: A:R.217

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 5 residues within 4Å: Chain B: W.128, L.155, E.178, V.182, R.217 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.128, B:V.182 Hydrogen bonds: B:S.176, B:S.176, B:R.217 Water bridges: B:R.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Romanaggi, C.T. et al., Crystal Structure of S-adenosyl-L-homocysteine hydrolase from Acanthamoeba castellanii with bound NAD and Adenosine. to be published

Release Date

2019-10-16

Peptides

Adenosylhomocysteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Adenosylhomocysteinase

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