SMTL ID : 4o9k.1

Crystal structure of the CBS pair of a putative D-arabinose 5-phosphate isomerase from Methylococcus capsulatus in complex with CMP-Kdo

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x CMK: CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID(Non-covalent)

CMK.1: 22 residues within 4Å: Chain A: V.54, T.56, G.58, D.59, R.61, R.62, T.80, S.82, C.83, V.84, R.103, I.104, N.105, A.106, L.107, P.108 Chain B: K.38, L.39, G.40, D.57, N.120, H.122 22 PLIP interactions: 7 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:L.39, B:D.57, B:D.57, B:N.120, A:T.56, A:G.58, A:D.59, A:D.59, A:R.62, A:V.84, A:V.84, A:N.105 Water bridges: B:L.39, B:D.57, B:R.126, A:R.61, A:R.61, A:N.105 Hydrophobic interactions: A:I.104 Salt bridges: A:R.61, A:R.62, A:R.62 CMK.3: 21 residues within 4Å: Chain A: K.38, G.40, N.120, H.122 Chain B: V.54, T.56, G.58, D.59, R.61, R.62, T.80, S.82, C.83, V.84, R.103, I.104, N.105, A.106, L.107, P.108 Ligands: GOL.2 22 PLIP interactions: 19 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.104 Hydrogen bonds: B:T.56, B:G.58, B:D.59, B:D.59, B:R.62, B:V.84, B:V.84, B:R.103, B:N.105, A:N.120 Water bridges: B:D.57, B:R.61, B:R.61, B:N.105, B:N.105, B:N.105, A:D.57, A:D.57 Salt bridges: B:R.61, B:R.62, B:R.62

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain B: K.102, R.103 Ligands: CMK.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shabalin, I.G. et al., Crystal structure and kinetic properties of D-arabinose 5-phosphate isomerase from Methylococcus capsulatus. To be Published

Release Date

2014-01-22

Peptides

Arabinose 5-phosphate isomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Arabinose 5-phosphate isomerase