SMTL ID : 4kx5.1

Cytosolic 5'-nucleotidase III complexed with cytidine 5'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.1: 17 residues within 4Å: Chain A: D.49, F.50, N.51, T.66, H.68, N.69, E.96, W.113, Y.114, S.117, S.164, A.165, G.166, V.210, K.213 Ligands: EDO.6, MG.14 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.114 Hydrogen bonds: A:D.49, A:D.49, A:F.50, A:N.51, A:N.51, A:T.66, A:N.69, A:E.96, A:S.117, A:S.117, A:A.165 Water bridges: A:C.67, A:K.213, A:K.213 Salt bridges: A:K.213 pi-Stacking: A:H.68, A:W.113

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 4 residues within 4Å: Chain A: A.7, C.34, I.37, K.38 No protein-ligand interaction detected (PLIP) BME.3: 6 residues within 4Å: Chain A: Y.59, K.62, R.63, C.64, D.139, M.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.59

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 3 residues within 4Å: Chain A: Q.294, K.295, L.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.294 Salt bridges: A:K.295

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 7 residues within 4Å: Chain A: A.41, A.42, H.156, G.157, I.158, P.159, N.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.156, A:N.230, A:N.230 EDO.6: 7 residues within 4Å: Chain A: R.63, T.66, N.69, K.89, Y.93, W.113 Ligands: C5P.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.63, A:T.66, A:N.69 Water bridges: A:C.64, A:N.69, A:K.89 EDO.7: 8 residues within 4Å: Chain A: D.98, L.101, T.102, V.103, K.106, F.211, Q.240, K.271 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.101 Water bridges: A:E.96, A:K.106, A:K.106, A:S.239 EDO.8: 3 residues within 4Å: Chain A: I.95, L.101, Y.109 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.109, A:Y.109 EDO.9: 4 residues within 4Å: Chain A: K.128, D.169, E.172, F.191 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.128, A:D.169, A:E.172 Water bridges: A:E.172, A:R.176 EDO.10: 2 residues within 4Å: Chain A: S.183, N.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.183 EDO.11: 5 residues within 4Å: Chain A: K.18, E.144, E.283, E.284, S.285 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.18, A:K.18, A:R.56, A:E.144 Water bridges: A:R.56, A:E.284, A:E.284 EDO.12: 4 residues within 4Å: Chain A: V.140, M.141, L.142, A.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.142, A:L.142 EDO.13: 3 residues within 4Å: Chain A: T.27, R.28, E.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.28

1 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 4 residues within 4Å: Chain A: D.49, N.51, D.238 Ligands: C5P.1 6 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.49, A:N.51, A:D.238, H2O.1, H2O.1, C5P.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bitto, E. et al., Cytosolic 5'-nucleotidase III complexed with cytidine 5'-monophosphate. TO BE PUBLISHED

Release Date

2013-06-12

Peptides

Cytosolic 5'-nucleotidase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytosolic 5'-nucleotidase 3

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