SMTL ID : 3n9w.1

Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) in complex with 1,2-Propanediol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.1: 8 residues within 4Å: Chain A: D.105, R.108, A.162, T.164, Q.166, D.189, K.212 Chain B: T.139 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.139, A:D.105, A:R.108 Hydrophobic interactions: A:T.164, A:D.189 PGO.2: 5 residues within 4Å: Chain A: A.134, R.137, H.161, L.163, A.208 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.134, A:H.161, A:A.208 Hydrogen bonds: A:R.137, A:R.137 Water bridges: A:R.108, A:N.210

1 x PGR: R-1,2-PROPANEDIOL(Non-covalent)

PGR.3: 6 residues within 4Å: Chain A: D.138, T.139 Chain B: D.105, R.108, A.162, K.212 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.139, A:T.139, B:R.108, B:R.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Behnen, J. et al., Experimental and computational active site mapping as a starting point to fragment-based lead discovery. Chemmedchem (2012)

Release Date

2011-05-25

Peptides

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase