SMTL ID : 5l6h.1 (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-1-1-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: 6O2.13 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.478 Water bridges: A:R.481, A:R.481, A:R.481, A:Q.482 Salt bridges: A:R.21, A:R.481

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

CL.2: 2 residues within 4Å: Chain A: T.571, K.572 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: R.861 Chain B: R.74 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: R.96 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: L.114, V.117 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 11 residues within 4Å: Chain A: D.282, K.285, F.391, D.392, S.393, E.395, L.876, L.879, E.880, K.895, F.908 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.282, A:S.393 Water bridges: A:D.392, A:E.395 GOL.7: 5 residues within 4Å: Chain A: R.288, N.344, D.346, L.347, L.394 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.288, A:N.344 GOL.8: 10 residues within 4Å: Chain A: L.134, K.137, S.153, S.154, E.155, N.162, L.273, F.296, Q.297, H.300 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.137, A:S.153, A:N.162, A:N.162 Water bridges: A:Q.297 GOL.9: 5 residues within 4Å: Chain A: L.635, L.811, A.812, G.813, F.814 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.813, A:G.813, A:F.814 GOL.10: 6 residues within 4Å: Chain A: L.737, Y.740, V.819, N.828, H.829, H.830 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Y.740, A:D.820, A:D.825, A:D.825 GOL.11: 2 residues within 4Å: Chain A: R.713, F.846 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.714 GOL.12: 4 residues within 4Å: Chain A: Y.24, Q.853, K.854, F.857 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.24

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)

6O2.13: 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, Y.551 Chain B: G.76 Ligands: SO4.1 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.548, A:Y.551 Hydrogen bonds: A:G.443, A:A.444, A:N.471, A:K.494, A:V.520, A:V.520, A:N.545, B:G.76 Water bridges: A:I.445, A:R.481, A:R.481, A:R.481, A:R.481, 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: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ubiquitin-activating enzyme E1 1

Ubiquitin-40S ribosomal protein S31

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