SMTL ID : 7zee.1

Human cytosolic 5' nucleotidase IIIB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 6 residues within 4Å: Chain A: E.90, W.107, W.108, A.111, T.204 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.90 pi-Cation interactions: A:W.108

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.43, D.45, D.232 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.43, A:D.45, A:D.232, H2O.2, H2O.3, H2O.7

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

EDO.3: 4 residues within 4Å: Chain A: Q.19, P.20, G.21, R.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.21 EDO.4: 6 residues within 4Å: Chain A: G.35, D.36, N.150, N.151, I.152, K.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.224, A:K.224 EDO.5: 7 residues within 4Å: Chain A: D.66, L.79, A.111, H.112, L.115, I.161 Ligands: MES.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.66 Water bridges: A:H.112 EDO.6: 3 residues within 4Å: Chain A: P.153, N.178, H.180 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.151, A:N.151 EDO.7: 3 residues within 4Å: Chain A: T.14, E.275, K.276 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain A: K.122, F.123, G.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.123 Water bridges: A:Q.121, A:G.192 EDO.9: 3 residues within 4Å: Chain A: K.122, D.163, E.167 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.167, A:E.167, A:R.170 Water bridges: A:D.163, A:D.163 EDO.10: 2 residues within 4Å: Chain A: Y.148, N.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.151, A:N.151 Water bridges: A:N.151 EDO.11: 4 residues within 4Å: Chain A: E.106, T.109, K.110, N.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.113 EDO.12: 7 residues within 4Å: Chain A: S.61, Y.62, S.158, G.160, I.161, I.164, L.165 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.158, A:I.161 Water bridges: A:Y.62 EDO.13: 5 residues within 4Å: Chain A: K.141, N.145, M.172, K.173, V.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.145, A:N.145, A:M.172 EDO.14: 4 residues within 4Å: Chain A: V.129, S.132, A.134, Q.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.134, A:Q.171 EDO.15: 3 residues within 4Å: Chain A: H.84, Y.87, P.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.84 Water bridges: A:H.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kubacka, D. et al., Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism. Pharmaceuticals (2022)

Release Date

2022-04-13

Peptides

7-methylguanosine phosphate-specific 5'-nucleotidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

7-methylguanosine phosphate-specific 5'-nucleotidase

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