SMTL ID : 8qq3.1

Streptavidin with a Ni-cofactor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x WKF: 4-[4-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]butylamino]-~{N}1,~{N}1'-di(quinolin-8-yl)cyclohexane-1,1-dicarboxamide(Non-covalent)

WKF.1: 25 residues within 4Å: Chain A: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, S.88, T.90, W.92, W.108, S.112, T.114, K.121, S.122, T.123, L.124, D.128 Chain C: W.120, K.121, L.124 Ligands: NI.2, WKF.5 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:N.49, A:W.79, A:W.79, A:T.114, A:L.124, A:L.124, A:L.124, C:K.121, C:L.124 Hydrogen bonds: A:N.23, A:S.27, A:S.45, A:N.49, A:S.112, A:D.128 WKF.3: 25 residues within 4Å: Chain B: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, S.88, T.90, W.92, W.108, L.110, S.112, T.114, K.121, S.122, T.123, L.124, D.128 Chain D: W.120, K.121, L.124 Ligands: NI.4 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:N.49, B:W.79, B:W.79, B:L.110, B:T.114, B:K.121, B:L.124, B:L.124, D:K.121 Hydrogen bonds: B:N.23, B:S.27, B:S.45, B:N.49, B:S.112, B:D.128 WKF.5: 25 residues within 4Å: Chain A: W.120, L.124 Chain C: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, S.88, T.90, W.92, W.108, L.110, S.112, T.114, K.121, S.122, T.123, L.124, D.128 Ligands: WKF.1, NI.6 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:N.49, C:W.79, C:W.79, C:L.110, C:T.114, C:L.124, C:L.124, A:L.124 Hydrogen bonds: C:N.23, C:S.27, C:Y.43, C:S.45, C:N.49, C:S.112, C:D.128 WKF.7: 13 residues within 4Å: Chain B: W.120 Chain D: N.23, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, T.90, W.92, W.108, D.128 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.79, D:W.79 Hydrogen bonds: D:N.23, D:S.27, D:Y.43, D:S.45, D:N.49, D:D.128

3 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 2 residues within 4Å: Chain A: S.112 Ligands: WKF.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.112 NI.4: 2 residues within 4Å: Chain B: S.112 Ligands: WKF.3 No protein-ligand interaction detected (PLIP) NI.6: 2 residues within 4Å: Chain C: S.112 Ligands: WKF.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, K. et al., An artificial nickel chlorinase based on the biotin-streptavidin technology. Chem.Commun.(Camb.) (2024)

Release Date

2024-02-07

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Streptavidin

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