SMTL ID : 3kp1.2 (1 other biounit)

Crystal structure of ornithine 4,5 aminomutase (Resting State)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-2-2-mer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 12 residues within 4Å: Chain A: K.626, H.627 Chain C: R.109, G.112, Q.113, S.114, Y.160, S.162, Y.187, R.192, H.222, N.223 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Y.187, A:K.626 Hydrogen bonds: C:G.112, C:S.114, C:S.114, C:S.162, C:Y.187, C:H.222, C:N.223 Water bridges: C:R.109, A:H.627 Salt bridges: C:R.109, C:R.192 pi-Stacking: C:Y.187 PLP.4: 14 residues within 4Å: Chain A: R.109, A.111, G.112, Q.113, S.114, Y.160, S.162, H.182, Y.187, R.192, H.222, N.223 Chain C: K.626, H.627 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.187, C:K.626 Hydrogen bonds: A:G.112, A:Q.113, A:S.114, A:S.114, A:S.162, A:H.222, A:N.223 Water bridges: A:T.110 Salt bridges: A:R.109, A:R.192 pi-Stacking: A:Y.160, A:Y.187

2 x B12: COBALAMIN(Non-covalent)

B12.2: 29 residues within 4Å: Chain A: E.612, D.613, E.614, H.615, S.616, V.617, G.618, L.619, V.622, L.662, A.663, S.664, I.666, I.667, S.668, H.669, G.698, G.699, T.700, F.716, G.717, G.719, S.720, V.725 Chain C: H.115, Y.116, I.127, D.487 Ligands: 5AD.6 31 PLIP interactions: 24 interactions with chain A, 7 interactions with chain C, Hydrophobic interactions: A:V.617, A:V.622, A:L.662, A:I.666, A:F.716, A:F.716, A:V.725, C:Y.116 Hydrogen bonds: A:E.612, A:E.614, A:S.616, A:S.616, A:V.617, A:G.618, A:S.668, A:S.668, A:H.669, A:G.699, A:T.700, A:T.700, A:G.719 Water bridges: A:S.616, A:T.700, A:S.720, C:Y.116, C:Y.116, C:Y.116, C:D.490, C:D.490, C:D.490 Metal complexes: A:H.615 B12.5: 30 residues within 4Å: Chain A: H.115, Y.116, I.127, D.487 Chain C: E.612, D.613, E.614, H.615, S.616, V.617, G.618, L.619, E.621, V.622, L.662, A.663, S.664, I.666, I.667, S.668, H.669, G.696, G.698, G.699, T.700, F.716, G.717, S.720, V.725 Ligands: 5AD.3 25 PLIP interactions: 22 interactions with chain C, 3 interactions with chain A, Hydrophobic interactions: C:E.621, C:V.622, C:V.622, C:L.662, C:I.666, C:F.716, C:F.716, C:V.725, A:Y.116 Hydrogen bonds: C:E.612, C:D.613, C:E.614, C:S.616, C:S.616, C:V.617, C:G.618, C:S.668, C:S.668, C:H.669, C:T.700, C:T.700 Water bridges: C:G.719, A:Q.125, A:D.490 Metal complexes: C:H.615

2 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.3: 2 residues within 4Å: Chain A: L.486 Ligands: B12.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.487 5AD.6: 3 residues within 4Å: Chain C: E.121, L.486 Ligands: B12.2 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wolthers, K.R. et al., Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase. J.Biol.Chem. (2010)

Release Date

2010-01-26

Peptides

D-ornithine aminomutase E component: AC
D-ornithine aminomutase S component: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
D

B
F

D
H

D-ornithine aminomutase E component

D-ornithine aminomutase S component

Related Entries With Identical Sequence