SMTL ID : 9cbt.2 (1 other biounit)

Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.139, C.142, C.163, C.166 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.139, A:C.142, A:C.163, A:C.166

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 4 residues within 4Å: Chain A: P.209, S.212, L.213, A.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.209

1 x 5I7: (phenylmethyl) ~{N}-[(2~{S})-6-[[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-6-oxidanyl-2-tridecyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]amino]-1-oxidanylidene-1-[2-(triethyl-$l^{4}-azanyl)ethylamino]hexan-2-yl]carbamate(Non-covalent)

5I7.3: 37 residues within 4Å: Chain A: G.28, A.29, G.30, T.33, P.34, I.37, D.39, F.40, R.41, S.42, L.47, Y.48, F.63, L.82, Y.87, Q.111, I.113, H.131, I.174, V.175, F.176, F.177, G.178, E.179, P.180, L.181, G.202, T.203, S.204, V.207, E.208, P.209, N.227, R.228, G.247, D.248, V.249 42 PLIP interactions: 42 interactions with chain A Hydrophobic interactions: A:I.37, A:L.47, A:F.63, A:L.82, A:Y.87, A:I.174, A:V.175, A:F.177, A:P.180, A:L.181, A:V.207 Hydrogen bonds: A:A.29, A:T.33, A:D.39, A:D.39, A:F.40, A:R.41, A:R.41, A:R.41, A:Q.111, A:H.131, A:V.175, A:G.178, A:E.179, A:T.203, A:T.203, A:S.204, A:S.204, A:S.204, A:E.208, A:N.227, A:R.228, A:R.228, A:R.228, A:D.229, A:D.248, A:V.249 Water bridges: A:S.42, A:Q.111 Salt bridges: A:R.41 pi-Cation interactions: A:R.228, A:R.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenwick, M.K. et al., Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10. To Be Published

Release Date

2024-08-07

Peptides

NAD-dependent protein deacetylase sirtuin-3, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

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