SMTL ID : 9csw.1

Streptavidin-E101Q-S112A-K121Y bound to Cu(II)-biotin-ethyl-dipicolylamine cofactor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

4 x QG7: N-(2-{bis[(pyridin-2-yl)methyl]amino}ethyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide(Non-covalent)

QG7.1: 23 residues within 4Å: Chain A: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, A.112, L.124, D.128 Chain C: W.120, Y.121 Ligands: ACY.3, CU.4 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:A.50, A:W.79, A:W.79, A:W.79, A:L.110, A:A.112, C:W.120, C:W.120, C:Y.121, C:Y.121 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:N.49, A:S.88, A:S.88, A:D.128 QG7.5: 23 residues within 4Å: Chain B: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, A.112, L.124, D.128 Chain D: W.120, Y.121 Ligands: ACY.7, CU.8 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:A.50, B:W.79, B:W.79, B:W.79, B:L.110, B:A.112, D:W.120, D:W.120, D:Y.121, D:Y.121 Hydrogen bonds: B:N.23, B:S.27, B:S.45, B:N.49, B:S.88, B:S.88, B:D.128 QG7.9: 23 residues within 4Å: Chain A: W.120, Y.121 Chain C: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, A.112, L.124, D.128 Ligands: ACY.11, CU.12 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:A.50, C:W.79, C:W.79, C:W.79, C:L.110, C:A.112, A:W.120, A:W.120, A:Y.121, A:Y.121 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:N.49, C:S.88, C:S.88, C:D.128 QG7.13: 23 residues within 4Å: Chain B: W.120, Y.121 Chain D: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, A.86, S.88, T.90, W.92, W.108, L.110, A.112, L.124, D.128 Ligands: ACY.15, CU.16 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:A.50, D:W.79, D:W.79, D:W.79, D:L.110, D:A.112, B:W.120, B:W.120, B:Y.121, B:Y.121 Hydrogen bonds: D:N.23, D:S.27, D:S.45, D:N.49, D:S.88, D:S.88, D:D.128

8 x CU: COPPER (II) ION(Non-covalent)(Non-functional Binders)

CU.2: 1 residues within 4Å: Chain A: H.87 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.87, H2O.4 CU.4: 2 residues within 4Å: Ligands: QG7.1, ACY.3 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: ACY.3, H2O.4 CU.6: 1 residues within 4Å: Chain B: H.87 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.87, H2O.8 CU.8: 2 residues within 4Å: Ligands: QG7.5, ACY.7 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: ACY.7, H2O.8 CU.10: 1 residues within 4Å: Chain C: H.87 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.87, H2O.12 CU.12: 2 residues within 4Å: Ligands: QG7.9, ACY.11 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: ACY.11, H2O.12 CU.14: 1 residues within 4Å: Chain D: H.87 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.87, H2O.16 CU.16: 2 residues within 4Å: Ligands: QG7.13, ACY.15 No protein-ligand interaction detected (PLIP)

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 3 residues within 4Å: Chain A: N.49 Ligands: QG7.1, CU.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.49 ACY.7: 3 residues within 4Å: Chain B: N.49 Ligands: QG7.5, CU.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.49 ACY.11: 3 residues within 4Å: Chain C: N.49 Ligands: QG7.9, CU.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.49 ACY.15: 3 residues within 4Å: Chain D: N.49 Ligands: QG7.13, CU.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Uyeda, K.S. et al., Selective oxidation of active site aromatic residues in engineered Cu proteins. Chem Sci (2024)

Release Date

2024-12-11

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Streptavidin