SMTL ID : 1xrs.1

Crystal structure of Lysine 5,6-Aminomutase in complex with PLP, cobalamin, and 5'-deoxyadenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-oligomer

Ligands

2 x B12: COBALAMIN(Non-covalent)

B12.1: 30 residues within 4Å: Chain A: Y.193 Chain B: T.130, D.131, A.132, H.133, T.134, V.135, G.136, I.140, Y.146, Q.166, L.185, V.186, S.187, T.189, V.190, T.191, Q.192, L.219, C.220, G.221, G.222, P.223, F.239, G.240, P.241, R.243, F.244, V.248 Ligands: 5AD.3 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:V.135, B:I.140, B:Y.146, B:L.185, B:T.189, B:F.239, B:F.239, B:V.248 Hydrogen bonds: B:T.130, B:D.131, B:A.132, B:H.133, B:T.134, B:T.134, B:V.135, B:T.191, B:T.191, B:Q.192, B:R.243 pi-Stacking: B:H.133 Metal complexes: B:H.133 B12.4: 30 residues within 4Å: Chain C: Y.193 Chain D: T.130, D.131, A.132, H.133, T.134, V.135, G.136, I.140, Y.146, Q.166, L.185, V.186, S.187, T.189, V.190, T.191, Q.192, L.219, C.220, G.221, G.222, P.223, F.239, G.240, P.241, R.243, F.244, V.248 Ligands: 5AD.6 22 PLIP interactions: 22 interactions with chain D, Hydrophobic interactions: D:V.135, D:I.140, D:Y.146, D:L.185, D:T.189, D:F.239, D:F.239, D:V.248 Hydrogen bonds: D:T.130, D:A.132, D:H.133, D:H.133, D:T.134, D:T.134, D:T.134, D:V.135, D:T.191, D:T.191, D:Q.192, D:R.243 pi-Stacking: D:H.133 Metal complexes: D:H.133

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

PLP.2: 12 residues within 4Å: Chain A: R.184, T.186, G.187, Q.188, S.189, Y.236, S.238, L.258, Y.263, R.268, N.299 Chain B: K.144 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.236, A:L.258, A:Y.263, B:K.144 Hydrogen bonds: A:G.187, A:S.189, A:S.189, A:S.189, A:S.238, A:N.299 Salt bridges: A:R.184, A:R.268, B:K.144 pi-Stacking: A:Y.263 PLP.5: 12 residues within 4Å: Chain C: R.184, T.186, G.187, Q.188, S.189, Y.236, S.238, L.258, Y.263, R.268, N.299 Chain D: K.144 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.236, C:L.258, C:Y.263, D:K.144 Hydrogen bonds: C:G.187, C:S.189, C:S.189, C:S.189, C:S.238, C:Y.263, C:N.299, D:K.144 Salt bridges: C:R.184, C:R.268, D:K.144 pi-Stacking: C:Y.263

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

5AD.3: 6 residues within 4Å: Chain A: D.54, E.55, V.56, D.64, Y.193 Ligands: B12.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.54, A:E.55, A:D.64 5AD.6: 6 residues within 4Å: Chain C: D.54, E.55, V.56, D.64, Y.193 Ligands: B12.4 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.54, C:E.55, C:D.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berkovitch, F. et al., A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase. Proc.Natl.Acad.Sci.Usa (2004)

Release Date

2004-11-09

Peptides

D-lysine 5,6-aminomutase alpha subunit: AC
D-lysine 5,6-aminomutase beta subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

D-lysine 5,6-aminomutase alpha subunit

D-lysine 5,6-aminomutase beta subunit