SMTL ID : 5l6i.1 (1 other biounit)

Uba1 in complex with Ub-MLN4924 covalent adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 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: B39.18 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.478 Water bridges: A:R.481, A:R.481 Salt bridges: A:R.21, A:R.481

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

CL.2: 2 residues within 4Å: Chain A: R.96, A.97 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: H.300 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: E.180 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: K.28, E.29 Ligand excluded by PLIP CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: F.821 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: E.822 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: R.861 Chain B: R.74 Ligand excluded by PLIP

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.282, A:K.285 Water bridges: A:D.392, A:D.392, A:L.876, A:E.880 GOL.10: 5 residues within 4Å: Chain A: Y.740, V.819, N.828, H.829, H.830 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.828 Water bridges: A:N.828 GOL.11: 9 residues within 4Å: Chain A: K.137, S.153, E.155, N.162, L.273, H.293, F.296, Q.297, Y.390 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.153, A:S.153, A:E.155, A:N.162, A:H.293 GOL.12: 3 residues within 4Å: Chain A: R.288, N.344, D.346 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.288, A:N.344 Water bridges: A:R.288 GOL.13: 5 residues within 4Å: Chain A: L.134, E.135, V.138, L.273, Q.297 No protein-ligand interaction detected (PLIP) GOL.14: 5 residues within 4Å: Chain A: L.114, D.115, V.117, D.136, K.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.114 GOL.15: 8 residues within 4Å: Chain A: K.33, R.150, F.171, T.172, L.174, C.378, S.379, G.380 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.150, A:T.172, A:C.378 GOL.16: 3 residues within 4Å: Chain A: D.851, R.852, Q.853 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.852, A:R.852, A:Q.853 GOL.17: 5 residues within 4Å: Chain A: R.554, V.557, F.558, E.1004, F.1019 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.554, A:F.558, A:E.1004

1 x B39: [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate(Covalent)

B39.18: 21 residues within 4Å: Chain A: G.441, G.443, A.444, D.470, N.471, D.472, R.481, Q.482, K.494, D.518, K.519, V.520, A.542, L.543, D.544, N.545, D.547, A.548, Y.551 Chain B: G.76 Ligands: SO4.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.543, A:A.548, A:Y.551 Hydrogen bonds: A:A.444, A:N.471, A:K.494, A:V.520, A:V.520 Water bridges: A:R.481, A:R.481 Salt bridges: A:R.481, A:K.494

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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