SMTL ID : 9e6z.1

Streptavidin-E101Q-S112F-K121A bound to Cu(II)-biotin-ethyl-dipicolylamine cofactor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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: 25 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, N.85, A.86, H.87, S.88, T.90, W.92, W.108, L.110, F.112, L.124, D.128 Chain C: W.120, A.121 Ligands: ACY.2, CU.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.79, A:W.79, A:W.79, A:L.110, A:L.124 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 QG7.4: 25 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, N.85, A.86, H.87, S.88, T.90, W.92, W.108, L.110, F.112, L.124, D.128 Chain D: W.120, A.121 Ligands: ACY.5, CU.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.79, B:W.79, B:W.79, B:L.110, B:L.124 Hydrogen bonds: B:N.23, B:S.27, B:S.45, B:N.49, B:S.88, B:S.88, B:D.128 QG7.7: 25 residues within 4Å: Chain A: W.120, A.121 Chain C: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, N.85, A.86, H.87, S.88, T.90, W.92, W.108, L.110, F.112, L.124, D.128 Ligands: ACY.8, CU.9 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.79, C:W.79, C:W.79, C:L.110, C:L.124 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 QG7.10: 25 residues within 4Å: Chain B: W.120, A.121 Chain D: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, A.50, W.79, N.85, A.86, H.87, S.88, T.90, W.92, W.108, L.110, F.112, L.124, D.128 Ligands: ACY.11, CU.12 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.79, D:W.79, D:W.79, D:L.110, D:L.124 Hydrogen bonds: D:N.23, D:S.27, D:S.45, D:N.49, D:S.88, D:S.88, D:D.128

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

ACY.2: 2 residues within 4Å: Ligands: QG7.1, CU.3 No protein-ligand interaction detected (PLIP) ACY.5: 2 residues within 4Å: Ligands: QG7.4, CU.6 No protein-ligand interaction detected (PLIP) ACY.8: 2 residues within 4Å: Ligands: QG7.7, CU.9 No protein-ligand interaction detected (PLIP) ACY.11: 2 residues within 4Å: Ligands: QG7.10, CU.12 No protein-ligand interaction detected (PLIP)

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

CU.3: 2 residues within 4Å: Ligands: QG7.1, ACY.2 2 PLIP interactions: 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, ACY.2 CU.6: 2 residues within 4Å: Ligands: QG7.4, ACY.5 2 PLIP interactions: 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.3, ACY.5 CU.9: 2 residues within 4Å: Ligands: QG7.7, ACY.8 2 PLIP interactions: 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.6, ACY.8 CU.12: 2 residues within 4Å: Ligands: QG7.10, ACY.11 2 PLIP interactions: 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.9, ACY.11

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

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