SMTL ID : 2d0p.1

Structure of diol dehydratase-reactivating factor in nucleotide free form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-2-2-mer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: G.10, N.11, S.12, S.13, D.413 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.11, A:S.12, A:S.13, A:S.13 SO4.2: 6 residues within 4Å: Chain A: N.11, G.415, A.416, G.417, S.418 Ligands: SO4.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.11, A:N.11, A:A.416, A:G.417, A:S.418, A:S.418 Salt bridges: A:K.41 SO4.3: 2 residues within 4Å: Chain A: R.518, R.522 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.518, A:R.522 SO4.5: 2 residues within 4Å: Chain C: R.518, R.522 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.518, C:R.522 SO4.6: 6 residues within 4Å: Chain C: N.11, D.413, G.415, A.416, G.417, S.418 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.11, C:A.416, C:G.417, C:S.418

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: T.105, D.166, D.183, E.184 Chain B: E.31 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Metal complexes: A:T.105, A:T.105, A:D.166, A:D.183, B:E.31 CA.7: 5 residues within 4Å: Chain C: T.105, D.166, D.183, E.184 Chain D: E.31 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Metal complexes: C:T.105, C:T.105, C:D.166, C:D.183, D:E.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shibata, N. et al., Release of a damaged cofactor from a coenzyme B12-dependent enzyme: X-ray structures of diol dehydratase-reactivating factor. Structure (2005)

Release Date

2006-02-28

Peptides

diol dehydratase-reactivating factor large subunit: AC
diol dehydratase-reactivating factor small subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

diol dehydratase-reactivating factor large subunit

diol dehydratase-reactivating factor small subunit

Related Entries With Identical Sequence