SMTL ID : 8cwp.1

X-ray crystal structure of NTHi Protein D bound to a putative glycerol moiety

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 8 residues within 4Å: Chain A: H.22, E.49, D.51, H.64, E.157, K.159, Q.194 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.51, A:Q.194 NA.3: 8 residues within 4Å: Chain B: H.22, E.49, D.51, H.64, E.157, K.159, Q.194 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.157, B:E.157, B:Q.194

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 14 residues within 4Å: Chain A: H.22, R.23, E.49, D.51, H.64, E.157, K.159, Q.194, F.196, L.221, Y.300, T.301, F.331 Ligands: NA.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.64, A:K.159, A:Q.194, A:Q.194 Water bridges: A:R.23, A:T.301, A:T.301 GOL.4: 14 residues within 4Å: Chain B: H.22, R.23, E.49, D.51, H.64, E.157, K.159, Q.194, F.196, L.221, Y.300, T.301, F.331 Ligands: NA.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.64, B:K.159, B:Q.194, B:Q.194 Water bridges: B:R.23, B:T.301, B:T.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, S.P. et al., Vaccine target and carrier molecule nontypeable Haemophilus influenzae protein D dimerizes like the close Escherichia coli GlpQ homolog but unlike other known homolog dimers. Proteins (2023)

Release Date

2022-09-28

Peptides

Glycerophosphoryl diester phosphodiesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycerophosphoryl diester phosphodiesterase