SMTL ID : 7bay.1

Crystal structure of CbpF from Streptococcus pneumoniae complexed with a Ytterbium derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

6 x CHT: CHOLINE ION(Non-covalent)

CHT.1: 6 residues within 4Å: Chain A: W.194, W.201, Y.222, M.231, S.248 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A pi-Cation interactions: A:W.194, A:W.194, A:W.201, A:W.201 CHT.2: 6 residues within 4Å: Chain A: W.163, W.181, Y.202, M.210, K.227, N.228 4 PLIP interactions: 4 interactions with chain A pi-Cation interactions: A:W.163, A:W.163, A:W.181, A:W.181 CHT.3: 5 residues within 4Å: Chain A: W.235, W.242, Y.263, M.272, S.289 4 PLIP interactions: 4 interactions with chain A pi-Cation interactions: A:W.235, A:W.235, A:W.242, A:W.242 CHT.5: 6 residues within 4Å: Chain A: W.255, W.262, Y.284, L.292, N.306 Ligands: GOL.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.306, A:N.306 pi-Cation interactions: A:W.255, A:W.255, A:W.262, A:W.262 CHT.6: 6 residues within 4Å: Chain A: W.214, W.221, Y.243, M.251, G.268, N.269 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.269 pi-Cation interactions: A:W.214, A:W.214, A:W.221, A:W.221 CHT.8: 5 residues within 4Å: Chain A: W.130, W.137, Y.182, M.190, S.207 4 PLIP interactions: 4 interactions with chain A pi-Cation interactions: A:W.130, A:W.130, A:W.137, A:W.137

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 9 residues within 4Å: Chain A: Y.203, F.204, G.205, S.206, S.207, S.209, M.210, A.211, K.215 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.206, A:S.206, A:K.215

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: Q.257, W.262, Y.305, N.306 Ligands: CHT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.257, A:W.262 GOL.9: 5 residues within 4Å: Chain A: Y.244, R.246, S.247, S.248, Y.256 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.244, A:R.246, A:S.247, A:S.247 GOL.10: 5 residues within 4Å: Chain A: K.196, W.201, S.247, S.248 Ligands: CHT.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.196, A:W.201, A:S.247

1 x T7K: neutral Yb(III)-caged complex(Non-covalent)

T7K.11: 4 residues within 4Å: Chain A: W.276, W.283, Y.301, W.309 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions pi-Cation interactions: A:W.276, A:W.276, A:W.283, A:W.283, A:W.283, A:W.309 Metal complexes: T7K.11, T7K.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prieto-Castaneda, A. et al., First Lanthanide Complex for De Novo Phasing in Native Protein Crystallography at 1 angstrom Radiation. Acs Appl Bio Mater (2021)

Release Date

2021-07-21

Peptides

Choline-binding protein F: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

Choline-binding protein F

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