SMTL ID : 2oyn.1

Crystal structure of CDP-bound protein MJ0056 from Methanococcus jannaschii, Pfam DUF120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: T.45, N.47 Ligands: CDP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.45, A:T.45 Water bridges: A:N.47 NA.3: 3 residues within 4Å: Chain B: T.45, N.47 Ligands: CDP.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.45, B:T.45, B:T.45 Water bridges: B:N.47

2 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.2: 17 residues within 4Å: Chain A: S.15, G.16, L.17, G.18, E.19, G.20, R.21, Y.42, G.44, T.45, L.46, A.112, M.114, K.115, L.116, R.117 Ligands: NA.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.16, A:G.16, A:G.18, A:G.18, A:E.19, A:G.20, A:R.21, A:T.45, A:A.112, A:M.114, A:L.116, A:R.117, A:R.117 Water bridges: A:T.45, A:R.117 Salt bridges: A:R.21, A:R.21 pi-Stacking: A:Y.42 CDP.4: 17 residues within 4Å: Chain B: S.15, G.16, L.17, G.18, E.19, G.20, R.21, Y.42, G.44, T.45, L.46, A.112, M.114, K.115, L.116, R.117 Ligands: NA.3 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:G.16, B:G.16, B:G.18, B:G.18, B:E.19, B:E.19, B:G.20, B:R.21, B:T.45, B:A.112, B:M.114, B:L.116, B:R.117, B:R.117 Water bridges: B:Y.42, B:T.45, B:N.47, B:R.117 Salt bridges: B:R.21, B:R.21 pi-Stacking: B:Y.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonanno, J.B. et al., Crystal structure of hypothetical protein from Methanococcus jannaschii bound to CDP. TO BE PUBLISHED

Release Date

2007-03-06

Peptides

Hypothetical protein MJ0056: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hypothetical protein MJ0056