SMTL ID : 6zht.1

Uba1-Ubc13 disulfide mediated complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 13 residues within 4Å: Chain A: L.111, K.114, S.130, E.132, N.139, F.141, L.246, L.250, F.273, Q.274, H.277, F.365, Y.367 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.130, A:N.139 Water bridges: A:Q.274 GOL.2: 6 residues within 4Å: Chain A: P.499, E.502, R.532, Y.936, G.937, I.979 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.502 Water bridges: A:R.532 GOL.3: 10 residues within 4Å: Chain A: D.507, E.511, F.535, Y.536, R.537, R.907, D.909, T.977, T.998, H.1000 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.907 Water bridges: A:R.537, A:R.907 GOL.4: 5 residues within 4Å: Chain A: K.549, F.875, N.877, L.880, F.882 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.877 GOL.5: 9 residues within 4Å: Chain A: R.531, R.532, V.534, F.535, I.979, E.981, F.996 Chain B: A.3, S.4 No protein-ligand interaction detected (PLIP) GOL.6: 5 residues within 4Å: Chain A: K.22, E.46, R.68, D.107, T.108 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.22, A:R.68, A:R.68 Water bridges: A:D.107, A:T.108 GOL.7: 6 residues within 4Å: Chain A: K.407, A.410, N.411, S.437, G.438, S.439 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.411, A:S.439, A:S.439 GOL.8: 7 residues within 4Å: Chain A: L.91, D.92, D.93, V.94, D.113, K.116, I.117 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.116 GOL.9: 4 residues within 4Å: Chain A: A.591, K.594, S.595, Q.598 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.595, A:S.595, A:Q.598 GOL.10: 4 residues within 4Å: Chain A: D.909, I.910, K.911, H.1000 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.910 GOL.11: 11 residues within 4Å: Chain A: V.417, G.418, T.446, D.447, N.448, D.495, K.496, V.497, L.520, N.522, A.525 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.448, A:D.495, A:V.497, A:N.522 GOL.16: 8 residues within 4Å: Chain A: P.575, L.576, C.577 Chain B: I.87, C.88, L.89, L.92, K.93 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.89, B:L.89, B:K.93, B:K.93

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

CL.12: 6 residues within 4Å: Chain A: Q.349, L.352, K.353, S.356, K.358, F.359 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: F.187, K.206 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: D.107, R.134, L.287 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: Y.394, L.403, Q.406, K.407 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Misra, M. et al., ATP induced conformational changes facilitate E1-E2 disulfide bridging in the ubiquitin system. To Be Published

Release Date

2022-01-12

Peptides

Ubiquitin-activating enzyme E1 1: A
Ubiquitin-conjugating enzyme E2 13: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

Ubiquitin-activating enzyme E1 1

Ubiquitin-conjugating enzyme E2 13