SMTL ID : 7zof.1

Streptavidin Iron-Porphyrin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

2 x JLL: (2R)-2-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-3-[[(5Z,10Z,14Z,19Z)-15-[[[(2R)-2-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-3-sulfo-propanoyl]amino]methyl]-1,4,21,23-tetrahydroporphyrin-5-yl]methylamino]-3-oxidanylidene-propane-1-sulfonic acid(Non-covalent)

JLL.1: 40 residues within 4Å: Chain A: N.22, L.24, S.26, Y.42, S.44, V.46, G.47, N.48, W.78, A.85, S.87, T.89, W.91, W.107, L.109, W.119, L.123, D.127 Chain C: N.22, L.24, S.26, Y.42, S.44, V.46, G.47, N.48, W.78, A.85, S.87, T.89, W.91, W.107, L.109, W.119, A.120, L.123, D.127 Ligands: IMD.2, IMD.5, FE.6 27 PLIP interactions: 13 interactions with chain A, 14 interactions with chain C Hydrophobic interactions: A:W.78, A:W.78, A:W.78, A:L.109, A:L.123, A:L.123, C:W.78, C:W.78, C:W.78, C:L.109, C:A.120, C:L.123 Hydrogen bonds: A:N.22, A:S.26, A:S.44, A:N.48, A:N.48, A:S.87, A:D.127, C:N.22, C:S.26, C:Y.42, C:S.44, C:N.48, C:N.48, C:S.87, C:D.127 JLL.3: 41 residues within 4Å: Chain B: N.22, L.24, S.26, Y.42, S.44, V.46, G.47, N.48, W.78, A.85, S.87, T.89, W.91, W.107, L.109, W.119, L.123, D.127 Chain D: N.22, L.24, S.26, Y.42, S.44, V.46, G.47, N.48, W.78, A.85, S.87, T.89, W.91, W.107, L.109, W.119, A.120, S.121, L.123, D.127 Ligands: IMD.4, IMD.7, FE.8 25 PLIP interactions: 12 interactions with chain D, 13 interactions with chain B Hydrophobic interactions: D:W.78, D:W.78, D:W.78, D:A.120, B:W.78, B:W.78, B:W.78, B:L.109, B:L.123, B:L.123 Hydrogen bonds: D:N.22, D:S.26, D:Y.42, D:S.44, D:N.48, D:N.48, D:S.87, D:D.127, B:N.22, B:S.26, B:S.44, B:G.47, B:N.48, B:S.87, B:D.127

4 x IMD: IMIDAZOLE(Non-covalent)(Non-functional Binders)

IMD.2: 6 residues within 4Å: Chain A: A.120, S.121, L.123 Chain C: L.123 Ligands: JLL.1, FE.6 No protein-ligand interaction detected (PLIP) IMD.4: 6 residues within 4Å: Chain B: A.120, S.121, L.123 Chain D: L.123 Ligands: JLL.3, FE.8 No protein-ligand interaction detected (PLIP) IMD.5: 2 residues within 4Å: Ligands: JLL.1, FE.6 No protein-ligand interaction detected (PLIP) IMD.7: 2 residues within 4Å: Ligands: JLL.3, FE.8 No protein-ligand interaction detected (PLIP)

2 x FE: FE (III) ION(Non-functional Binders)

FE.6: 3 residues within 4Å: Ligands: JLL.1, IMD.2, IMD.5 No protein-ligand interaction detected (PLIP) FE.8: 3 residues within 4Å: Ligands: JLL.3, IMD.4, IMD.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Igareta, N.V., Streptavidin Iron-Porphyrin. To Be Published

Release Date

2022-07-13

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Streptavidin

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