SMTL ID : 6uk3.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 29 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: Q.466, K.479, Y.483 Ligands: ADN.2 24 PLIP interactions: 19 interactions with chain A, 5 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: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:D.277, A:D.277, A:G.279, A:T.296 NAD.9: 30 residues within 4Å: Chain A: L.462, 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.10 23 PLIP interactions: 18 interactions with chain B, 5 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: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:D.277, B:D.277, B:G.279, B:T.296

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.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.76, A:T.77, A:T.211, A:T.211, A:K.240, A:K.240, A:H.408 ADN.10: 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.9, K.16 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.74, B:Q.76, B:T.77, B:T.211, B:K.240, B:K.240, B:H.408

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

ACT.3: 4 residues within 4Å: Chain A: L.155, S.176, E.178, R.217 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.178 Water bridges: A:R.217 Salt bridges: A:R.217 ACT.4: 4 residues within 4Å: Chain A: S.426, E.430, P.440, L.443 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.440 Hydrogen bonds: A:E.430 ACT.12: 5 residues within 4Å: Chain B: L.155, S.176, L.179, V.182, R.217 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.179, B:V.182 Hydrogen bonds: B:S.176, B:R.217 Water bridges: B:D.152, B:R.217 ACT.15: 4 residues within 4Å: Chain B: S.426, E.430, P.440, L.443 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.440 Hydrogen bonds: B:E.430 Water bridges: B:S.426

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

FMT.5: 1 residues within 4Å: Chain A: Y.162 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.159 FMT.6: 1 residues within 4Å: Chain A: F.34 No protein-ligand interaction detected (PLIP) FMT.8: 3 residues within 4Å: Chain A: H.346, N.347, Q.382 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.347, A:Q.382 Water bridges: A:Q.382 FMT.11: 3 residues within 4Å: Chain B: H.346, N.347, Q.382 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.346, B:N.347, B:Q.382 FMT.13: 3 residues within 4Å: Chain B: H.158, R.159, Y.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.158 Water bridges: B:R.159 FMT.14: 3 residues within 4Å: Chain B: K.199, P.202, E.203 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.203, B:E.203

2 x K: POTASSIUM ION(Non-covalent)

K.7: 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.10, H2O.12 K.16: 5 residues within 4Å: Chain B: Q.76, T.406, G.407, H.408 Ligands: ADN.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.406, B:T.406, B:H.408, H2O.32, H2O.34

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
B

B
D

Adenosylhomocysteinase

Related Entries With Identical Sequence