SMTL ID : 5v1m.1

Structure of human Usb1 with uridine 5'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: V.36, P.37, R.38 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: Q.65, K.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.68 GOL.3: 6 residues within 4Å: Chain A: H.10, Y.12, V.44, H.46, K.180, F.185 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.45, A:R.178 GOL.4: 5 residues within 4Å: Chain A: A.66, A.69, R.70, V.118, E.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.70, A:R.70, A:E.121 GOL.5: 4 residues within 4Å: Chain A: Q.65, K.68, A.69, T.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.65, A:A.69 GOL.6: 6 residues within 4Å: Chain A: T.80, N.82, Q.83, T.102, S.103, L.170 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.82, A:N.82, A:Q.83 Water bridges: A:N.82, A:T.102 GOL.7: 6 residues within 4Å: Chain A: P.14, Y.15, E.16, E.175, Q.176, R.178 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.175, A:E.175, A:Q.176 Water bridges: A:E.16, A:A.17

1 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.8: 13 residues within 4Å: Chain A: H.46, S.48, Y.87, T.88, N.89, Q.90, F.96, F.127, Y.128, P.131, S.132, H.134, S.136 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.48, A:Q.90, A:Q.90, A:Y.128, A:S.132, A:H.134, A:H.134, A:S.136 Water bridges: A:H.10, A:H.10, A:H.10, A:H.46, A:H.46, A:T.88, A:D.130, A:H.134, A:S.136 Salt bridges: A:H.46, A:H.134 pi-Stacking: A:Y.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Didychuk, A.L. et al., Usb1 controls U6 snRNP assembly through evolutionarily divergent cyclic phosphodiesterase activities. Nat Commun (2017)

Release Date

2017-08-16

Peptides

U6 snRNA phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

U6 snRNA phosphodiesterase

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