SMTL ID : 6een.1

Crystal structure of a designer Pentatrico Peptide RNA binding protein, bound to a complex RNA target and featuring an infinite superhelix and microheterogeneity.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x G- G- G- G- G- G- G- G- G: RNA (5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')(Non-covalent)

G-G-G-G-G-G-G-G-G.1: 282 residues within 4Å: Chain A: V.1, V.2, T.5, T.6, D.9, K.13, D.35, V.36, V.37, T.40, T.41, D.44, K.48, D.70, V.71, V.72, T.73, T.75, T.76, D.79, K.83, D.105, V.106, V.107, T.110, T.111, D.114, K.118, D.140, V.141, V.142, T.145, T.146, D.149, K.153, D.175, V.176, V.177, T.180, T.181, D.184, K.188, D.210, V.211, V.212, T.213, T.215, T.216, D.219, K.223, D.245, V.246, V.247, T.248, T.250, T.251, D.254, K.258, D.280, V.281, V.282, T.285, T.286, D.315 Chain B: V.1, V.2, N.5, T.6, D.9, K.13, D.35, V.36, V.37, T.38, N.40, T.41, D.44, K.48, D.70, V.71, V.72, T.73, N.75, T.76, D.79, K.83, D.105, V.106, V.107, N.110, T.111, D.114, K.118, D.140, V.141, V.142, N.145, T.146, D.149, K.153, D.175, V.176, V.177, N.180, T.181, D.184, K.188, D.210, V.211, V.212, N.215, T.216, D.219, K.223, D.245, V.246, V.247, N.250, T.251, D.254, K.258, D.280, V.281, V.282, N.285, T.286, D.315 Chain C: V.1, V.2, T.5, T.6, D.9, K.13, N.35, V.36, V.37, T.40, T.41, D.44, K.48, N.70, V.71, V.72, T.73, T.75, T.76, D.79, K.83, N.105, V.106, V.107, T.110, T.111, D.114, K.118, N.140, V.141, V.142, T.145, T.146, D.149, K.153, N.175, V.176, V.177, T.180, T.181, D.184, K.188, N.210, V.211, V.212, T.213, T.215, T.216, D.219, K.223, N.245, V.246, V.247, T.248, T.250, T.251, D.254, K.258, N.280, V.281, V.282, T.285, T.286, N.315 Chain D: V.1, V.2, N.5, T.6, D.9, K.13, S.35, V.36, V.37, T.38, N.40, T.41, D.44, K.48, S.70, V.71, V.72, T.73, N.75, T.76, D.79, K.83, S.105, V.106, V.107, N.110, T.111, D.114, K.118, S.140, V.141, V.142, N.145, T.146, D.149, K.153, S.175, V.176, V.177, N.180, T.181, D.184, K.188, S.210, V.211, V.212, N.215, T.216, D.219, K.223, S.245, V.246, V.247, T.248, N.250, T.251, D.254, K.258, S.280, V.281, V.282, N.285, T.286, S.315 Ligands: U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4 Protein-ligand interaction information (PLIP) not available

1 x U- U- U- U- U- U- U- U- U: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')(Non-covalent)

U-U-U-U-U-U-U-U-U.2: 199 residues within 4Å: Chain A: V.2, T.5, T.6, D.9, K.13, V.37, T.40, T.41, D.44, K.48, V.72, T.75, T.76, D.79, K.83, V.107, T.110, T.111, D.114, K.118, V.142, T.145, T.146, D.149, K.153, V.177, T.180, T.181, D.184, K.188, V.212, T.215, T.216, D.219, K.223, V.247, T.250, T.251, D.254, K.258, V.282, T.285, T.286 Chain B: V.2, N.5, T.6, D.9, K.13, V.37, N.40, T.41, D.44, K.48, V.72, N.75, T.76, D.79, K.83, V.107, N.110, T.111, D.114, K.118, V.142, N.145, T.146, D.149, K.153, V.177, N.180, T.181, D.184, K.188, V.212, N.215, T.216, D.219, K.223, V.247, N.250, T.251, D.254, K.258, V.282, N.285, T.286 Chain C: V.2, T.5, T.6, D.9, K.13, V.37, T.40, T.41, D.44, K.48, V.72, T.75, T.76, D.79, K.83, V.107, T.110, T.111, D.114, K.118, V.142, T.145, T.146, D.149, K.153, V.177, T.180, T.181, D.184, K.188, V.212, T.215, T.216, D.219, K.223, V.247, T.250, T.251, D.254, K.258, V.282, T.285, T.286 Chain D: V.2, N.5, T.6, D.9, K.13, V.37, N.40, T.41, D.44, K.48, V.72, N.75, T.76, D.79, K.83, V.107, N.110, T.111, D.114, K.118, V.142, N.145, T.146, D.149, K.153, V.177, N.180, T.181, D.184, K.188, V.212, N.215, T.216, D.219, K.223, V.247, N.250, T.251, D.254, K.258, V.282, N.285, T.286 Ligands: G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4 Protein-ligand interaction information (PLIP) not available

1 x A- A- A- A- A- A- A- A- A: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')(Non-covalent)

A-A-A-A-A-A-A-A-A.3: 229 residues within 4Å: Chain A: V.2, T.5, T.6, D.9, K.13, D.35, V.37, T.40, T.41, D.44, K.48, D.70, V.72, T.75, T.76, D.79, K.83, D.105, V.107, T.110, T.111, D.114, K.118, D.140, V.142, T.145, T.146, D.149, K.153, D.175, V.177, T.180, T.181, D.184, K.188, D.210, V.212, T.215, T.216, D.219, K.223, D.245, V.247, T.250, T.251, D.254, K.258, D.280, V.282, T.285, T.286, D.315 Chain B: V.2, N.5, T.6, D.9, K.13, D.35, V.37, N.40, T.41, D.44, K.48, D.70, V.72, N.75, T.76, D.79, K.83, D.105, V.107, N.110, T.111, D.114, K.118, D.140, V.142, N.145, T.146, D.149, K.153, D.175, V.177, N.180, T.181, D.184, K.188, D.210, V.212, N.215, T.216, D.219, K.223, D.245, V.247, N.250, T.251, D.254, K.258, D.280, V.282, N.285, T.286, D.315 Chain C: V.2, T.5, T.6, D.9, K.13, N.35, V.37, T.40, T.41, D.44, K.48, N.70, V.72, T.75, T.76, D.79, K.83, N.105, V.107, T.110, T.111, D.114, K.118, N.140, V.142, T.145, T.146, D.149, K.153, N.175, V.177, T.180, T.181, D.184, K.188, N.210, V.212, T.215, T.216, D.219, K.223, N.245, V.247, T.250, T.251, D.254, K.258, N.280, V.282, T.285, T.286, N.315 Chain D: V.2, N.5, T.6, D.9, K.13, V.37, N.40, T.41, D.44, K.48, V.72, N.75, T.76, D.79, K.83, S.105, V.107, N.110, T.111, D.114, K.118, V.142, N.145, T.146, D.149, K.153, V.177, N.180, T.181, D.184, K.188, V.212, N.215, T.216, D.219, K.223, V.247, N.250, T.251, D.254, K.258, S.280, V.282, N.285, T.286, S.315 Ligands: G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4, C-C-C-C-C-C-C-C-C.4 Protein-ligand interaction information (PLIP) not available

1 x C- C- C- C- C- C- C- C- C: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')(Non-covalent)

C-C-C-C-C-C-C-C-C.4: 199 residues within 4Å: Chain A: V.2, T.5, T.6, D.9, K.13, V.37, T.40, T.41, D.44, K.48, V.72, T.75, T.76, D.79, K.83, V.107, T.110, T.111, D.114, K.118, V.142, T.145, T.146, D.149, K.153, V.177, T.180, T.181, D.184, K.188, V.212, T.215, T.216, D.219, K.223, V.247, T.250, T.251, D.254, K.258, V.282, T.285, T.286 Chain B: V.2, N.5, T.6, D.9, K.13, V.37, N.40, T.41, D.44, K.48, V.72, N.75, T.76, D.79, K.83, V.107, N.110, T.111, D.114, K.118, V.142, N.145, T.146, D.149, K.153, V.177, N.180, T.181, D.184, K.188, V.212, N.215, T.216, D.219, K.223, V.247, N.250, T.251, D.254, K.258, V.282, N.285, T.286 Chain C: V.2, T.5, T.6, D.9, K.13, V.37, T.40, T.41, D.44, K.48, V.72, T.75, T.76, D.79, K.83, V.107, T.110, T.111, D.114, K.118, V.142, T.145, T.146, D.149, K.153, V.177, T.180, T.181, D.184, K.188, V.212, T.215, T.216, D.219, K.223, V.247, T.250, T.251, D.254, K.258, V.282, T.285, T.286 Chain D: V.2, N.5, T.6, D.9, K.13, V.37, N.40, T.41, D.44, K.48, V.72, N.75, T.76, D.79, K.83, V.107, N.110, T.111, D.114, K.118, V.142, N.145, T.146, D.149, K.153, V.177, N.180, T.181, D.184, K.188, V.212, N.215, T.216, D.219, K.223, V.247, N.250, T.251, D.254, K.258, V.282, N.285, T.286 Ligands: G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, G-G-G-G-G-G-G-G-G.1, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, U-U-U-U-U-U-U-U-U.2, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3, A-A-A-A-A-A-A-A-A.3 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidberger, J.W. et al., Crystal structure of a designer Pentatrico Peptide RNA binding protein, bound to a complex RNA target and featuring an infinite superhelix and microheterogeneity. To Be Published

Release Date

2019-08-21

Peptides

Designer Pentatricopeptide Protein dPPR10: A
Designer Pentatricopeptide Protein dPPR10: B
Designer Pentatricopeptide Protein dPPR10: C
Designer Pentatricopeptide Protein dPPR10: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Designer Pentatricopeptide Protein dPPR10

Designer Pentatricopeptide Protein dPPR10

Designer Pentatricopeptide Protein dPPR10

Designer Pentatricopeptide Protein dPPR10