SMTL ID : 4nnj.1

Crystal structure of Uba1 in complex with ubiquitin-AMP and thioesterified ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-3-mer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: R.37, N.494, R.497, D.560, K.839, I.878 Ligands: AMP.20 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.494 Water bridges: A:R.497, A:R.497, A:R.497, A:Q.498, A:D.560, A:K.839 Salt bridges: A:R.37, A:R.497 SO4.19: 4 residues within 4Å: Chain A: G.43, K.44, E.45, K.397 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.44, A:E.45 Water bridges: A:G.43, A:K.397 Salt bridges: A:K.397 SO4.21: 8 residues within 4Å: Chain C: R.37, S.493, N.494, R.497, K.839, I.879 Ligands: GOL.31, AMP.35 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.494 Water bridges: C:Q.498, C:D.560, C:D.560, C:K.839 Salt bridges: C:R.37, C:R.497 SO4.34: 5 residues within 4Å: Chain C: D.216, R.218 Chain D: Q.34, G.38 Chain E: R.45 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 2 interactions with chain C Hydrogen bonds: D:Q.34, C:D.216 Salt bridges: E:R.45, C:R.218

29 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 13 residues within 4Å: Chain A: L.150, K.153, S.169, E.171, N.178, L.285, L.289, H.309, F.312, Q.313, H.316, F.404, Y.406 Ligand excluded by PLIP GOL.3: 11 residues within 4Å: Chain A: D.298, K.301, F.407, D.408, S.409, E.411, L.892, L.895, E.896, K.911, F.924 Ligand excluded by PLIP GOL.4: 10 residues within 4Å: Chain A: K.49, R.166, E.186, F.187, T.188, L.190, A.393, C.394, S.395, G.396 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: Y.481, V.483, N.530, F.548 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: R.304, N.360, D.362, L.363, E.366, L.410 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: S.752, L.753, Y.756, V.835, D.836, N.844, H.845, H.846 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: E.550, F.574, Y.575, R.576, R.946, D.948, T.1037, H.1039 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: Y.40, E.196, D.867, Q.869, K.870, F.873 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: M.330, K.365, E.366, Y.369, P.416, P.420, R.421 Ligand excluded by PLIP GOL.11: 8 residues within 4Å: Chain A: V.148, S.149, L.150, R.173, H.316, A.319, G.324, L.326 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: T.851, D.867, R.868, Q.869 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain A: E.45, L.48, K.49, T.52 Chain C: E.45, L.48, K.49, T.52 Ligand excluded by PLIP GOL.14: 8 residues within 4Å: Chain A: A.515, E.516, C.519, L.525, K.526, G.527, K.528, I.529 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: E.231, R.729, A.730, F.862 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain A: R.570, V.573, F.574, I.943, I.1018, E.1020, F.1035 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain A: L.130, V.133, D.152, K.155, I.156 Chain C: Y.739 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain A: D.737, Y.739 Chain C: V.154, K.155, E.158, K.286 Ligands: GOL.30 Ligand excluded by PLIP GOL.22: 11 residues within 4Å: Chain C: D.298, K.301, F.407, D.408, S.409, E.411, L.892, L.895, E.896, K.911, F.924 Ligand excluded by PLIP GOL.23: 13 residues within 4Å: Chain C: L.150, K.153, S.169, E.171, N.178, L.285, L.289, H.309, F.312, Q.313, H.316, F.404, Y.406 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain C: T.971, S.983, D.1024, G.1028, D.1030 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain C: L.753, Y.756, V.835, D.836, N.844, H.845, H.846 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain C: R.304, N.360, D.362, L.363, E.366, L.410 Ligand excluded by PLIP GOL.27: 8 residues within 4Å: Chain C: Y.40, V.41, L.42, G.43, D.191, G.194, K.397 Ligands: GOL.28 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain C: G.43, K.44, E.45, K.397 Ligands: GOL.27 Ligand excluded by PLIP GOL.29: 9 residues within 4Å: Chain C: E.550, F.574, Y.575, R.576, R.946, D.948, T.1016, T.1037, H.1039 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain C: L.150, E.151, V.154, K.286, L.289 Ligands: GOL.18 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain C: D.488, D.560, N.561 Ligands: SO4.21, AMP.35 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain A: Y.739, D.772 Chain C: L.130, D.131, V.133, D.152, K.155, I.156 Ligand excluded by PLIP GOL.33: 10 residues within 4Å: Chain C: K.49, R.166, E.186, F.187, T.188, L.190, A.393, C.394, S.395, G.396 Ligand excluded by PLIP

2 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.20: 22 residues within 4Å: Chain A: V.456, G.457, S.458, G.459, A.460, T.485, D.486, N.487, D.488, R.497, Q.498, K.510, D.534, K.535, V.536, A.558, L.559, D.560, N.561, A.564 Chain B: G.79 Ligands: SO4.1 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.459, A:A.460, A:D.488, A:Q.498, A:K.510, A:V.536, A:V.536, A:N.561, B:G.79 Water bridges: A:I.461, A:R.497, A:R.497, A:R.497, A:R.497, A:R.497, A:D.560, A:D.560, A:A.564, A:A.564 Salt bridges: A:R.497, A:K.510 AMP.35: 23 residues within 4Å: Chain C: V.456, G.457, S.458, G.459, A.460, T.485, D.486, N.487, D.488, R.497, Q.498, K.510, D.534, K.535, V.536, A.558, L.559, D.560, N.561, A.564 Chain D: G.79 Ligands: SO4.21, GOL.31 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.459, C:A.460, C:D.488, C:Q.498, C:K.510, C:V.536, C:V.536, C:D.560, C:N.561, D:G.79 Water bridges: C:I.461, C:R.497, C:R.497, C:R.497, C:R.497, C:D.560, C:A.564, C:A.564 Salt bridges: C:R.497, C:K.510

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schafer, A. et al., Structure of the ubiquitin-activating enzyme loaded with two ubiquitin molecules. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-05-07

Peptides

Ubiquitin-activating enzyme E1 1: AC
Uba1: BDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

Ubiquitin-activating enzyme E1 1

Uba1