SMTL ID : 4coo.1

Crystal structure of human cystathionine beta-synthase (delta516-525) at 2.0 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: P.71, S.72, R.73, C.74, T.75, W.76, R.80, E.84, S.85, P.86, H.87, R.246, A.248, P.251, L.252, Y.255, G.285, R.288, T.335, V.336 Ligands: EDO.4 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:R.73, A:A.248, A:P.251, A:L.252, A:Y.255, A:Y.255, A:V.336 Hydrogen bonds: A:R.73 Salt bridges: A:R.73, A:R.73, A:R.246 pi-Cation interactions: A:R.288 Metal complexes: A:C.74, A:H.87 HEM.12: 22 residues within 4Å: Chain B: P.71, S.72, R.73, C.74, T.75, W.76, R.80, P.81, E.84, S.85, P.86, H.87, R.246, A.248, P.251, L.252, Y.255, G.285, R.288, T.335, V.336 Ligands: EDO.17 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:T.75, B:A.248, B:P.251, B:L.252, B:Y.255, B:Y.255, B:V.336 Hydrogen bonds: B:S.72, B:R.73 Salt bridges: B:R.73, B:R.73, B:R.246 pi-Cation interactions: B:R.288 Metal complexes: B:C.74, B:H.87

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 8 residues within 4Å: Chain A: K.141, T.168, S.169, G.170, N.171, T.172, Q.244 Ligands: PLP.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:K.141, A:N.171 Hydrogen bonds: A:T.168, A:S.169, A:G.170, A:T.172, A:T.172, A:Q.244 Water bridges: A:S.169 Salt bridges: A:K.141 ACT.13: 9 residues within 4Å: Chain B: K.141, T.168, S.169, G.170, N.171, T.172, Q.244, Y.330 Ligands: PLP.16 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:K.141, B:N.171 Hydrogen bonds: B:T.168, B:T.168, B:S.169, B:G.170, B:T.172, B:Q.244 Water bridges: B:S.169 Salt bridges: B:K.141 ACT.14: 3 residues within 4Å: Chain B: E.209, V.211 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.211 Salt bridges: B:R.186 ACT.15: 4 residues within 4Å: Chain B: W.431, L.551, L.552 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.552 Water bridges: B:L.552 ACT.19: 7 residues within 4Å: Chain A: I.210, V.211 Chain B: S.522, L.525, E.526, L.551 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.211 Water bridges: A:I.210

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

PLP.3: 16 residues within 4Å: Chain A: K.141, N.171, S.276, V.277, G.278, T.279, G.280, G.281, T.282, E.326, G.327, I.328, S.371, P.397, D.398 Ligands: ACT.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:K.141, A:I.328, A:P.397, A:D.398 Hydrogen bonds: A:N.171, A:G.278, A:T.279, A:G.280, A:G.281, A:T.282, A:T.282, A:T.282, A:S.371 Water bridges: A:T.279, A:T.279, A:I.283, A:E.326, A:D.398 Salt bridges: A:K.141 PLP.16: 17 residues within 4Å: Chain B: K.141, N.171, S.276, V.277, G.278, T.279, G.280, G.281, T.282, E.326, G.327, I.328, S.371, P.397, D.398, Y.403 Ligands: ACT.13 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:K.141, B:I.328, B:D.398 Hydrogen bonds: B:N.171, B:S.276, B:G.278, B:T.279, B:G.280, B:G.281, B:T.282, B:T.282, B:S.371 Water bridges: B:N.250, B:T.279, B:I.283, B:E.326, B:D.398 Salt bridges: B:K.141

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 9 residues within 4Å: Chain A: S.72, C.74, P.251, T.284, R.288, T.335, V.336, D.338 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.72, A:S.72, A:V.336 EDO.5: 7 residues within 4Å: Chain A: A.217, F.219, S.224, H.225, Y.330, D.331, F.332 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.225, A:H.225, A:D.331 EDO.6: 7 residues within 4Å: Chain A: R.186, I.188, E.209, V.211 Chain B: L.552 Ligands: ACT.15, ACT.19 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:L.552 Hydrogen bonds: A:E.209 EDO.7: 3 residues within 4Å: Chain A: K.507, Q.508, F.509 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.509 Water bridges: A:K.507 EDO.8: 5 residues within 4Å: Chain A: I.333, L.337, D.338, R.339, T.340 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.338, A:D.338, A:R.339, A:R.339, A:T.340 EDO.11: 4 residues within 4Å: Chain A: W.431, L.551, L.552 Ligands: ACT.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.186 EDO.17: 9 residues within 4Å: Chain B: S.72, C.74, P.251, T.284, R.288, T.335, V.336, D.338 Ligands: HEM.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.72, B:S.72

1 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.9: 3 residues within 4Å: Chain A: E.458, R.461, E.462 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.461

2 x NA: SODIUM ION(Non-functional Binders)

NA.10: 6 residues within 4Å: Chain A: K.194, M.195, V.325, E.326, G.327, I.328 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.194, A:V.325, A:G.327, A:I.328 NA.18: 6 residues within 4Å: Chain B: K.194, M.195, V.325, E.326, G.327, I.328 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.194, B:K.194, B:G.327, B:I.328

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mccorvie, T.J. et al., Inter-Domain Communication of Human Cystathionine Beta Synthase: Structural Basis of S-Adenosyl-L-Methionine Activation. J.Biol.Chem. (2014)

Release Date

2014-03-05

Peptides

CYSTATHIONINE BETA-SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CYSTATHIONINE BETA-SYNTHASE

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