SMTL ID : 4pcu.1

Crystal structure of delta516-525 E201S human cystathionine beta-synthase with AdoMet

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.58 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 21 residues within 4Å: Chain A: P.49, S.50, R.51, C.52, T.53, W.54, R.58, P.59, E.62, S.63, P.64, H.65, R.224, A.226, P.229, L.230, Y.233, G.263, R.266, T.313, V.314 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:T.53, A:P.64, A:A.226, A:P.229, A:L.230, A:Y.233, A:Y.233, A:V.314 Hydrogen bonds: A:P.49, A:R.51 Salt bridges: A:R.51, A:R.51, A:R.224 pi-Stacking: A:H.65 pi-Cation interactions: A:R.266 Metal complexes: A:C.52, A:H.65 HEM.4: 20 residues within 4Å: Chain B: P.49, S.50, R.51, C.52, T.53, W.54, P.59, E.62, S.63, P.64, H.65, R.224, A.226, P.229, L.230, Y.233, G.263, R.266, T.313, V.314 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:T.53, B:P.64, B:A.226, B:P.229, B:L.230, B:Y.233, B:Y.233, B:T.313, B:V.314 Hydrogen bonds: B:P.49, B:R.51 Salt bridges: B:R.51, B:R.51, B:R.224 pi-Stacking: B:H.65 pi-Cation interactions: B:R.266 Metal complexes: B:C.52, B:H.65

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

PLP.2: 15 residues within 4Å: Chain A: K.119, N.149, S.254, G.256, T.257, G.258, G.259, T.260, E.304, G.305, I.306, S.349, P.375, D.376, Y.381 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.119, A:P.375 Hydrogen bonds: A:K.119, A:N.149, A:G.256, A:T.257, A:G.258, A:T.260, A:T.260, A:T.260, A:I.261, A:S.349 Salt bridges: A:K.119 PLP.5: 14 residues within 4Å: Chain B: K.119, N.149, S.254, G.256, T.257, G.258, T.260, I.261, E.304, G.305, I.306, S.349, P.375, D.376 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:K.119 Hydrogen bonds: B:N.149, B:S.254, B:G.256, B:T.257, B:G.258, B:G.259, B:T.260, B:T.260, B:T.260, B:I.261, B:S.349 Salt bridges: B:K.119

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.3: 14 residues within 4Å: Chain A: A.421, P.422, L.423, G.442, F.443, D.444, Q.445, P.447, V.523, T.525, I.527, D.528 Chain B: G.442 Ligands: SAM.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:L.423, A:D.444, A:Q.445, A:Q.445, A:T.525, A:T.525, A:D.528 pi-Stacking: A:F.443, A:F.443 SAM.6: 13 residues within 4Å: Chain A: G.442, D.444 Chain B: P.422, L.423, G.442, F.443, D.444, Q.445, V.523, T.525, I.527, D.528 Ligands: SAM.3 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.423, B:L.423, B:D.444, B:D.444, B:Q.445, B:T.525, B:T.525, B:D.528, A:D.444 pi-Stacking: B:F.443, B:F.443

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ereno-Orbea, J. et al., Structural insight into the molecular mechanism of allosteric activation of human cystathionine beta-synthase by S-adenosylmethionine. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-09-24

Peptides

Cystathionine beta-synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cystathionine beta-synthase