SMTL ID : 6h78.4 (7 other biounits)

E1 enzyme for ubiquitin like protein activation.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 22 residues within 4Å: Chain A: G.45, G.47, G.48, F.68, D.69, Y.70, D.71, N.77, R.80, K.92, Y.114, N.115, I.116, T.117, C.146, V.147, D.148, N.149, A.152 Chain B: R.20 Ligands: MG.2, MG.4 24 PLIP interactions: 22 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.48, A:Y.70, A:D.71, A:N.77, A:K.92, A:K.92, A:N.115, A:I.116, A:N.149 Water bridges: A:G.47, A:V.49, A:Y.70, A:R.80, A:A.152, A:A.152, B:R.20 Salt bridges: A:R.80, A:R.80, A:R.80, A:K.92, A:K.92, B:R.20 pi-Stacking: A:Y.70, A:Y.70 ATP.8: 21 residues within 4Å: Chain A: R.20 Chain B: G.45, G.47, G.48, D.69, Y.70, D.71, N.77, R.80, K.92, Y.114, N.115, I.116, T.117, C.146, V.147, D.148, N.149, A.152 Ligands: MG.9, MG.11 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.48, B:Y.70, B:D.71, B:D.71, B:N.77, B:K.92, B:N.115, B:I.116 Water bridges: B:G.47, B:V.49, B:N.149, B:N.149, B:S.218, A:R.20 Salt bridges: B:R.80, B:R.80, B:R.80, B:K.92, B:K.92, A:R.20 pi-Stacking: B:Y.70, B:Y.70

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.148 Ligands: ATP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.148, H2O.1 MG.4: 3 residues within 4Å: Chain A: D.71, K.92 Ligands: ATP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.71, H2O.2 MG.9: 2 residues within 4Å: Chain B: D.148 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.148 MG.11: 2 residues within 4Å: Chain B: D.71 Ligands: ATP.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.71, H2O.3, H2O.3, H2O.4

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.191, C.194, C.268, C.273 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.191, A:C.194, A:C.268, A:C.273 ZN.10: 4 residues within 4Å: Chain B: C.191, C.194, C.268, C.273 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.191, B:C.194, B:C.268, B:C.273

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: N.161, E.162, N.272, Q.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.162 EDO.6: 6 residues within 4Å: Chain A: P.139, V.140, D.141, G.164, Q.165 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.141, A:D.141, A:G.164 EDO.7: 3 residues within 4Å: Chain A: L.163, G.164 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.163, A:Q.165 EDO.12: 6 residues within 4Å: Chain A: E.55, F.82, Q.84 Chain B: E.55, F.82, Q.84 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.55, A:Q.84, B:Q.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Soudah, N. et al., An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation. J.Mol.Biol. (2019)

Release Date

2018-10-31

Peptides

Ubiquitin-like modifier-activating enzyme 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Ubiquitin-like modifier-activating enzyme 5

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