SMTL ID : 9cst.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.13 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: 24 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, S.112, T.114, L.124, D.128 Chain C: W.120, A.121 Ligands: CU.2, CU.3 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.79, A:W.79, A:W.79, A:L.110, C:W.120 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:N.49, A:S.88, A:D.128 QG7.6: 24 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, S.112, T.114, L.124, D.128 Chain D: W.120, A.121 Ligands: CU.7, CU.8 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:W.79, B:W.79, B:W.79, B:L.110, D:W.120 Hydrogen bonds: B:N.23, B:S.27, B:Y.43, B:S.45, B:N.49, B:S.88, B:D.128 QG7.11: 24 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, A.86, S.88, T.90, W.92, W.108, L.110, S.112, T.114, L.124, D.128 Ligands: CU.12, CU.13 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.79, C:W.79, C:W.79, C:L.110, A:W.120 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:N.49, C:S.88, C:D.128 QG7.16: 24 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, A.86, S.88, T.90, W.92, W.108, L.110, S.112, T.114, L.124, D.128 Ligands: CU.17, CU.18 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:W.79, D:W.79, D:W.79, D:L.110, B:W.120 Hydrogen bonds: D:N.23, D:S.27, D:Y.43, D:S.45, D:N.49, D:S.88, D:D.128

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

CU.2: 2 residues within 4Å: Ligands: QG7.1, CU.3 No protein-ligand interaction detected (PLIP) CU.3: 3 residues within 4Å: Chain A: L.124 Ligands: QG7.1, CU.2 No protein-ligand interaction detected (PLIP) CU.4: 5 residues within 4Å: Chain A: H.127 Chain B: N.105, T.106, Q.107, H.127 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.127, H2O.4, H2O.4, H2O.7 CU.5: 1 residues within 4Å: Chain A: H.87 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.87 CU.7: 2 residues within 4Å: Ligands: QG7.6, CU.8 No protein-ligand interaction detected (PLIP) CU.8: 3 residues within 4Å: Chain B: L.124 Ligands: QG7.6, CU.7 No protein-ligand interaction detected (PLIP) CU.9: 5 residues within 4Å: Chain A: N.105, T.106, Q.107, H.127 Chain B: H.127 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.127, H2O.2, H2O.9, H2O.9 CU.10: 1 residues within 4Å: Chain B: H.87 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.87 CU.12: 2 residues within 4Å: Ligands: QG7.11, CU.13 No protein-ligand interaction detected (PLIP) CU.13: 3 residues within 4Å: Chain C: L.124 Ligands: QG7.11, CU.12 No protein-ligand interaction detected (PLIP) CU.14: 5 residues within 4Å: Chain C: H.127 Chain D: N.105, T.106, Q.107, H.127 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.127, H2O.14, H2O.14, H2O.17 CU.15: 1 residues within 4Å: Chain C: H.87 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.87 CU.17: 2 residues within 4Å: Ligands: QG7.16, CU.18 No protein-ligand interaction detected (PLIP) CU.18: 3 residues within 4Å: Chain D: L.124 Ligands: QG7.16, CU.17 No protein-ligand interaction detected (PLIP) CU.19: 5 residues within 4Å: Chain C: N.105, T.106, Q.107, H.127 Chain D: H.127 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.127, H2O.12, H2O.19, H2O.19 CU.20: 1 residues within 4Å: Chain D: H.87 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.87

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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