SMTL ID : 8r2p.1

YZwIdeal x16 a scaffold for cryo-EM of small proteins of interest crystallizing in space group 19 (P 21 21 21)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: S.156, G.157, T.158, F.187, H.188, G.189, E.245, E.250, D.278, V.280, Q.281, K.307 Chain B: T.338, T.339 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:E.245, A:V.280 Hydrogen bonds: A:G.157, A:T.158, A:E.250, A:Q.281, B:T.338, B:T.339, B:T.339 Water bridges: A:T.158, A:F.187, A:E.245, B:T.337, B:F.340, B:F.340 pi-Stacking: A:F.187 PLP.2: 14 residues within 4Å: Chain A: T.338, T.339 Chain B: S.156, G.157, T.158, F.187, H.188, G.189, E.245, E.250, D.278, V.280, Q.281, K.307 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.280, B:Q.281 Hydrogen bonds: B:G.157, B:T.158, B:E.250, B:Q.281, B:K.307, A:T.338, A:T.339 Water bridges: B:F.187, A:T.337, A:T.337, A:F.340 pi-Stacking: B:F.187 PLP.3: 14 residues within 4Å: Chain C: S.156, G.157, T.158, F.187, H.188, G.189, E.245, E.250, D.278, V.280, Q.281, K.307 Chain D: T.338, T.339 11 PLIP interactions: 2 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:T.339, D:T.339, C:S.156, C:G.157, C:T.158, C:Q.281, C:K.307 Hydrophobic interactions: C:E.245, C:V.280 Water bridges: C:E.250 pi-Stacking: C:F.187 PLP.4: 14 residues within 4Å: Chain C: T.338, T.339 Chain D: S.156, G.157, T.158, F.187, H.188, G.189, E.245, E.250, D.278, V.280, Q.281, K.307 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:V.280 Hydrogen bonds: D:S.156, D:G.157, D:T.158, D:Q.281, D:K.307, C:T.339, C:T.339 Water bridges: D:T.158, D:T.158, D:F.187, D:E.250, C:T.339, C:T.339 pi-Stacking: D:F.187

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

2024-11-13

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