SMTL ID : 7sh1.1

Class II UvrA protein - Ecm16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 16 residues within 4Å: Chain A: N.51, N.52, V.71, S.72, G.73, S.74, G.75, K.76, S.77, S.78, G.470, Y.693, L.694, Q.698, T.702 Ligands: MG.8 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.73, A:S.74, A:G.75, A:K.76, A:S.77, A:S.77, A:S.78, A:S.695, A:Q.698, A:T.702 Water bridges: A:N.51, A:N.51, A:S.72, A:K.76, A:S.77, A:S.77, A:S.77, A:S.77, A:Y.693, A:Y.693, A:S.695 Salt bridges: A:K.76 ADP.2: 15 residues within 4Å: Chain A: Y.382, L.383, R.387, T.391, H.521, N.522, V.541, A.542, G.543, S.544, G.545, K.546, S.547, S.548, G.779 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:R.387, A:N.522, A:G.543, A:G.543, A:S.544, A:G.545, A:K.546, A:S.547, A:S.547, A:S.548, A:S.548 Water bridges: A:R.387, A:R.387, A:R.387, A:T.391, A:K.546, A:K.546, A:S.547, A:S.547, A:S.547, A:S.547 Salt bridges: A:K.546 pi-Stacking: A:H.521, A:H.521 ADP.9: 16 residues within 4Å: Chain B: N.51, N.52, V.71, S.72, G.73, S.74, G.75, K.76, S.77, S.78, G.470, Y.693, L.694, Q.698, T.702 Ligands: MG.15 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.73, B:S.74, B:G.75, B:K.76, B:S.77, B:S.77, B:S.78, B:S.78, B:Q.698 Water bridges: B:K.76, B:K.76, B:S.77, B:S.695 Salt bridges: B:K.76 ADP.10: 15 residues within 4Å: Chain B: Y.382, L.383, R.387, T.391, H.521, N.522, V.541, A.542, G.543, S.544, G.545, K.546, S.547, S.548, G.779 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:R.387, B:G.543, B:G.543, B:S.544, B:G.545, B:K.546, B:S.547, B:S.547, B:S.548, B:S.548 Water bridges: B:R.387, B:R.387, B:T.391, B:K.546, B:K.546, B:S.547, B:S.547, B:S.547, B:S.547 Salt bridges: B:K.546 pi-Stacking: B:H.521, B:H.521

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.609, C.612, C.632, C.635 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.609, A:C.612, A:C.632, A:C.635 ZN.4: 4 residues within 4Å: Chain A: C.196, C.199, C.316, C.319 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.196, A:C.199, A:C.316, A:C.319 ZN.11: 5 residues within 4Å: Chain B: C.609, T.611, C.612, C.632, C.635 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.609, B:C.612, B:C.632, B:C.635 ZN.12: 4 residues within 4Å: Chain B: C.196, C.199, C.316, C.319 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.196, B:C.199, B:C.316, B:C.319

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

CL.5: 2 residues within 4Å: Chain A: R.494, H.495 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: V.596, K.597, L.600 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: R.499 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: T.578, G.581, L.583, E.584 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: S.547, I.550, D.727, V.758 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 2 residues within 4Å: Chain A: S.77 Ligands: ADP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.77, H2O.5, H2O.6, H2O.8 MG.15: 2 residues within 4Å: Chain B: S.77 Ligands: ADP.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.77, H2O.19, H2O.21, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gade, P. et al., Structural and functional analyses of the echinomycin resistance conferring protein Ecm16 from Streptomyces lasalocidi. Sci Rep (2023)

Release Date

2022-10-26

Peptides

Excinuclease ABC subunit UvrA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Excinuclease ABC subunit UvrA