SMTL ID : 5l6h.2 (1 other biounit)

Uba1 in complex with Ub-ABPA3 covalent adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-2-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.21, N.478, R.481 Ligands: 6O2.12 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.478 Water bridges: A:N.478, A:R.481, A:R.481, A:R.481, A:Q.482, A:D.544, A:I.863 Salt bridges: A:R.21, A:R.481

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

CL.2: 3 residues within 4Å: Chain A: G.570, T.571, K.572 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: N.514 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: R.861 Chain B: R.74 Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 1 residues within 4Å: Chain A: D.1008 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.1008, H2O.1, H2O.3

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: R.713, A.714, F.846 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.714, A:A.714 GOL.8: 4 residues within 4Å: Chain A: K.267, Q.271, S.274, N.275 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.271 GOL.9: 10 residues within 4Å: Chain A: D.282, K.285, F.391, D.392, S.393, E.395, L.879, E.880, K.895, F.908 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.282, A:K.285, A:E.880 Water bridges: A:D.392, A:S.393, A:E.395, A:E.880 GOL.10: 2 residues within 4Å: Chain A: R.288, N.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.288, A:N.344, A:N.344

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 4 residues within 4Å: Chain A: L.114, D.115, V.117, D.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.114

1 x 6O2: [(2~{R},3~{S},4~{R},5~{R})-5-[6-[(3-ethynylphenyl)amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl sulfamate(Covalent)

6O2.12: 21 residues within 4Å: Chain A: G.441, G.443, A.444, D.470, N.471, D.472, R.481, Q.482, K.494, K.519, V.520, P.522, A.542, L.543, D.544, N.545, D.547, A.548 Chain B: G.75, G.76 Ligands: SO4.1 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.547 Hydrogen bonds: A:G.443, A:A.444, A:N.471, A:D.472, A:D.472, A:K.494, A:V.520, A:V.520, A:D.544, A:N.545, B:G.76 Water bridges: A:I.445, A:R.481, A:R.481, A:Q.482, A:Q.482 Salt bridges: A:R.481, A:K.494 pi-Cation interactions: A:K.519

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Misra, M. et al., Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme. Structure (2017)

Release Date

2017-06-14

Peptides

Ubiquitin-activating enzyme E1 1: A
Ubiquitin-40S ribosomal protein S31: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

Ubiquitin-activating enzyme E1 1

Ubiquitin-40S ribosomal protein S31

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