SMTL ID : 5w0n.1 (2 other biounits)

Structure of human TUT7 catalytic module (CM) in complex with UMPNPP and U2 RNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.85, D.96, D.98 Ligands: 2KH.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.96, A:D.98, H2O.1

1 x 2KH: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine(Non-covalent)

2KH.2: 21 residues within 4Å: Chain A: F.83, G.84, S.85, N.88, G.91, F.92, S.95, D.96, D.98, A.165, N.168, T.169, K.190, S.207, S.208, Y.209, D.318, H.324, L.326 Ligands: MG.1, UPU.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.209 Hydrogen bonds: A:S.85, A:S.85, A:S.85, A:N.88, A:S.95, A:D.98, A:N.168, A:N.168, A:T.169, A:S.207, A:S.208, A:S.208, A:H.324 Water bridges: A:S.86, A:D.96, A:D.96, A:D.96, A:K.190, A:K.190, A:S.208 Salt bridges: A:K.190

1 x UPU: [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-4-HYDROXY-2-(HYDROXYMETHYL)TETRAHYDROFURAN-3-YL HYDROGEN (S)-PHOSPHATE(Non-covalent)

UPU.3: 21 residues within 4Å: Chain A: F.83, D.96, D.98, I.137, T.139, A.140, K.141, V.142, I.144, D.157, S.159, N.162, A.165, A.201, S.202, H.324, K.390, I.391, G.392, H.393 Ligands: 2KH.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.137, A:V.142 Hydrogen bonds: A:D.98, A:D.98, A:T.139, A:N.162, A:K.390, A:H.393 Water bridges: A:D.96, A:V.99, A:K.141, A:A.201, A:S.202, A:H.324

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: C.385, I.387, C.388, H.393, C.398, P.399 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.385, A:C.388, A:H.393, A:C.398

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 5 residues within 4Å: Chain A: S.331, M.334, P.380, D.382, R.383 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 2 residues within 4Å: Chain A: R.132, L.150 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Faehnle, C.R. et al., Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-06-28

Peptides

Terminal uridylyltransferase 7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Terminal uridylyltransferase 7

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