SMTL ID : 6h77.1 (1 other biounit)

E1 enzyme for ubiquitin like protein activation in complex with UBL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

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

ATP.1: 23 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, EDO.11 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.48, A:Y.70, A:D.71, A:N.77, A:K.92, A:N.115, A:I.116, A:N.149 Water bridges: A:V.49, A:Y.70, A:Y.70, A:D.71, A:D.71, A:D.71, A:N.77, A:A.152, A:A.152, B:R.20, 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.15: 22 residues within 4Å: Chain A: R.20 Chain B: 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 Ligands: MG.16, MG.18 27 PLIP interactions: 23 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.48, B:Y.70, B:D.71, B:N.77, B:K.92, B:N.115, B:I.116, B:D.148, B:N.149 Water bridges: B:D.71, B:K.92, B:K.92, B:K.92, B:A.152, B:A.152, B:A.216, A:R.20, A:R.20, 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 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.148, H2O.2, H2O.3 MG.4: 2 residues within 4Å: Chain A: D.71 Ligands: ATP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.71, H2O.1, H2O.1, H2O.1, H2O.3 MG.16: 2 residues within 4Å: Chain B: D.148 Ligands: ATP.15 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.148, H2O.7, H2O.8 MG.18: 2 residues within 4Å: Chain B: D.71 Ligands: ATP.15 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.71, H2O.6, H2O.6, H2O.6, H2O.8

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.17: 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

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

EDO.5: 7 residues within 4Å: Chain A: E.55, R.59, F.82, Q.84 Chain B: E.55, F.82 Ligands: EDO.6 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: V.52, E.55, L.81, F.82 Chain B: V.52, E.55, L.81, F.82 Ligands: EDO.5 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: S.178, G.179, Y.247, G.249, Y.250, N.251, P.258 Chain D: S.12, P.78 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: Q.254, D.255, F.256 Chain B: T.259 Chain D: P.14 Ligands: EDO.9 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: F.256, F.257 Chain B: F.256, F.257 Ligands: EDO.8 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: F.256, P.258, T.259 Ligand excluded by PLIP EDO.11: 9 residues within 4Å: Chain A: G.47, G.48, S.51, N.77, R.80, L.81, F.83, K.92 Ligands: ATP.1 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: Q.94, H.98, R.101 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Chain A: Q.123 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: E.110, H.112, H.124, R.128 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: G.171, V.172, S.173, G.179, H.180 Ligands: EDO.20 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain B: S.178, G.179, Y.247, G.249, Y.250, P.258 Chain C: S.12, P.78 Ligands: EDO.19 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: E.97, E.110, V.111 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: Y.114, E.120, N.121, H.124 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: I.185, P.186, E.188, Q.276, Y.280 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: D.148, F.150, R.153, E.206 Chain C: T.46 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: P.266, R.274, Q.277, E.278, K.281 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain A: M.260, S.261 Chain D: I.50, N.52, D.53, G.54, R.75 Ligand excluded by PLIP

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
Ubiquitin-fold modifier 1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
Q

D
T

Ubiquitin-like modifier-activating enzyme 5

Ubiquitin-fold modifier 1

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