SMTL ID : 8cpl.1

YZw2 a scaffold for cryo-EM of small proteins of interest

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-tetramer

Ligands

4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 13 residues within 4Å: Chain A: S.143, G.144, T.145, F.174, H.175, G.176, E.232, D.265, V.267, Q.268, K.294 Chain B: T.325, T.326 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:E.232, A:V.267 Hydrogen bonds: A:G.144, A:T.145, A:Q.268, A:K.294, B:T.326 Water bridges: A:S.143, A:F.174, A:E.232, A:R.420, A:R.420, B:N.142, B:T.324, B:T.326, B:F.327 pi-Stacking: A:F.174 PLP.2: 13 residues within 4Å: Chain A: T.325, T.326 Chain B: S.143, G.144, T.145, F.174, H.175, G.176, E.232, D.265, V.267, Q.268, K.294 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:E.232, B:V.267 Hydrogen bonds: B:G.144, B:T.145, B:Q.268, B:K.294, A:T.326, A:T.326 Water bridges: B:S.143, B:F.174, B:E.232, B:E.237, A:N.142, A:T.324, A:T.324, A:F.327 pi-Stacking: B:F.174 PLP.3: 13 residues within 4Å: Chain C: S.143, G.144, T.145, F.174, H.175, G.176, E.232, D.265, V.267, Q.268, K.294 Chain D: T.325, T.326 18 PLIP interactions: 13 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:E.232, C:V.267 Hydrogen bonds: C:S.143, C:G.144, C:T.145, C:Q.268, C:K.294, D:T.326, D:T.326 Water bridges: C:S.143, C:F.174, C:E.232, C:R.420, C:R.420, D:N.142, D:T.326, D:F.327 pi-Stacking: C:F.174 PLP.4: 13 residues within 4Å: Chain C: T.325, T.326 Chain D: S.143, G.144, T.145, F.174, H.175, G.176, E.232, D.265, V.267, Q.268, K.294 15 PLIP interactions: 4 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:T.326, C:T.326, D:S.143, D:G.144, D:T.145, D:Q.268, D:K.294 Water bridges: C:T.326, C:F.327, D:S.143, D:F.174, D:E.232 Hydrophobic interactions: D:E.232, D:V.267 pi-Stacking: D:F.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moche, M. et al., Engineered imaging scaffolds for cryo-EM of small proteins of interest. To Be Published

Release Date

2024-06-12

Peptides

Putrescine aminotransferase,Immunoglobulin G-binding protein A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putrescine aminotransferase,Immunoglobulin G-binding protein A