SMTL ID : 8stw.1

K384N HUMAN CYSTATHIONINE BETA-SYNTHASE (delta 411-551)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

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

PLP.1: 16 residues within 4Å: Chain A: K.76, N.106, S.211, V.212, G.213, T.214, G.215, G.216, T.217, E.261, G.262, I.263, S.306, P.332, D.333, Y.338 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.76, A:D.333 Hydrogen bonds: A:N.106, A:G.213, A:T.214, A:G.215, A:T.217, A:T.217, A:S.306 Water bridges: A:N.185, A:T.214, A:I.218 Salt bridges: A:K.76 PLP.3: 16 residues within 4Å: Chain B: K.76, N.106, S.211, V.212, G.213, T.214, G.215, G.216, T.217, E.261, G.262, I.263, S.306, P.332, D.333, Y.338 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:K.76 Hydrogen bonds: B:N.106, B:S.211, B:G.213, B:T.214, B:G.215, B:G.216, B:T.217, B:T.217, B:S.306 Water bridges: B:N.185, B:T.214, B:I.218 Salt bridges: B:K.76 PLP.5: 15 residues within 4Å: Chain C: K.76, N.106, S.211, V.212, G.213, T.214, G.215, G.216, T.217, G.262, I.263, S.306, P.332, D.333, Y.338 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:K.76, C:D.333 Hydrogen bonds: C:N.106, C:G.213, C:T.214, C:G.215, C:G.216, C:T.217, C:T.217, C:S.306 Water bridges: C:N.185, C:N.185, C:I.218 Salt bridges: C:K.76 PLP.7: 16 residues within 4Å: Chain D: K.76, N.106, S.211, V.212, G.213, T.214, G.215, G.216, T.217, E.261, G.262, I.263, S.306, P.332, D.333, Y.338 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:K.76, D:P.332 Hydrogen bonds: D:N.106, D:S.211, D:G.213, D:T.214, D:G.215, D:G.216, D:T.217, D:T.217, D:S.306 Water bridges: D:N.185, D:S.211, D:G.215, D:T.217 Salt bridges: D:K.76 PLP.9: 16 residues within 4Å: Chain E: K.76, N.106, S.211, V.212, G.213, T.214, G.215, G.216, T.217, E.261, G.262, I.263, S.306, P.332, D.333, Y.338 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:K.76, E:D.333 Hydrogen bonds: E:N.106, E:G.213, E:T.214, E:G.215, E:T.217, E:T.217, E:S.306 Water bridges: E:H.189, E:T.214, E:I.218 Salt bridges: E:K.76 PLP.11: 15 residues within 4Å: Chain F: K.76, N.106, S.211, V.212, G.213, T.214, G.215, G.216, T.217, G.262, I.263, S.306, P.332, D.333, Y.338 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:K.76, F:D.333 Hydrogen bonds: F:K.76, F:N.106, F:G.213, F:T.214, F:G.215, F:G.216, F:T.217, F:T.217, F:T.217, F:S.306 Water bridges: F:N.185, F:N.185, F:I.218 Salt bridges: F:K.76

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

HEM.2: 17 residues within 4Å: Chain A: S.7, R.8, C.9, T.10, W.11, R.15, E.19, S.20, P.21, H.22, A.183, P.186, L.187, Y.190, G.220, R.223, T.270 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:R.8, A:A.183, A:P.186, A:L.187, A:Y.190, A:Y.190 Hydrogen bonds: A:P.6, A:R.8 Salt bridges: A:R.8, A:R.8, A:R.181 pi-Cation interactions: A:R.223 Metal complexes: A:C.9, A:H.22 HEM.4: 17 residues within 4Å: Chain B: S.7, R.8, C.9, T.10, W.11, R.15, E.19, S.20, P.21, H.22, R.181, A.183, P.186, L.187, Y.190, G.220, R.223 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:R.15, B:A.183, B:P.186, B:L.187, B:Y.190, B:Y.190 Hydrogen bonds: B:R.8 Salt bridges: B:R.8, B:R.8 pi-Cation interactions: B:R.223 Metal complexes: B:C.9, B:H.22 HEM.6: 17 residues within 4Å: Chain C: S.7, R.8, C.9, T.10, W.11, R.15, P.16, E.19, S.20, P.21, H.22, A.183, P.186, L.187, Y.190, G.220, R.223 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:T.10, C:R.15, C:A.183, C:P.186, C:L.187, C:Y.190, C:Y.190 Hydrogen bonds: C:R.8, C:R.8 Salt bridges: C:R.8, C:R.8 pi-Cation interactions: C:R.223 Metal complexes: C:C.9, C:H.22 HEM.8: 17 residues within 4Å: Chain D: S.7, R.8, C.9, T.10, W.11, R.15, P.16, E.19, S.20, P.21, H.22, A.183, P.186, L.187, Y.190, G.220, R.223 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:R.8, D:P.21, D:A.183, D:P.186, D:L.187, D:Y.190, D:Y.190 Hydrogen bonds: D:S.7, D:R.8 Salt bridges: D:R.8, D:R.8 pi-Cation interactions: D:R.223 Metal complexes: D:C.9, D:H.22 HEM.10: 16 residues within 4Å: Chain E: S.7, R.8, C.9, T.10, W.11, R.15, S.20, P.21, H.22, R.181, A.183, P.186, L.187, Y.190, R.223, V.271 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:A.183, E:P.186, E:P.186, E:L.187, E:Y.190, E:Y.190, E:V.271 Hydrogen bonds: E:R.8 Salt bridges: E:R.8, E:R.8 pi-Cation interactions: E:R.223 Metal complexes: E:C.9, E:H.22 HEM.12: 17 residues within 4Å: Chain F: S.7, R.8, C.9, T.10, W.11, R.15, P.16, E.19, S.20, P.21, H.22, A.183, P.186, L.187, Y.190, G.220, R.223 14 PLIP interactions: 14 interactions with chain F, Hydrophobic interactions: F:R.15, F:P.21, F:A.183, F:P.186, F:L.187, F:Y.190, F:Y.190 Hydrogen bonds: F:R.8 Salt bridges: F:R.8, F:R.8, F:R.181 pi-Cation interactions: F:R.223 Metal complexes: F:C.9, F:H.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roman, J.V. et al., Disease-causing cystathionine beta-synthase linker mutations impair allosteric regulation. J.Biol.Chem. (2023)

Release Date

2023-11-22

Peptides

Cystathionine beta-synthase, K384N variant: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Cystathionine beta-synthase, K384N variant