SMTL ID : 8s5m.1

Full-length human cystathionine beta-synthase with C-terminal 6xHis-tag, SAM bound, activated state, helical reconstruction

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

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

SAM.1: 13 residues within 4Å: Chain A: A.421, L.423, G.442, F.443, D.444, Q.445, A.446, P.447, V.533, T.535, I.537, D.538 Chain B: R.439 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.423, A:L.423, A:D.444, A:Q.445, A:T.535, A:D.538 pi-Stacking: A:F.443, A:F.443 SAM.2: 15 residues within 4Å: Chain A: R.439, G.442 Chain B: L.419, A.421, L.423, G.442, F.443, D.444, Q.445, A.446, P.447, V.533, T.535, I.537, D.538 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:D.444 Hydrogen bonds: B:L.423, B:D.444, B:Q.445, B:Q.445, B:Q.445, B:T.535, B:T.535, B:D.538 SAM.3: 14 residues within 4Å: Chain C: S.420, A.421, L.423, G.442, F.443, D.444, Q.445, A.446, P.447, V.533, T.535, D.538 Chain D: R.439, G.442 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:L.423, C:D.444, C:Q.445, C:Q.445, C:Q.445, C:T.535, C:D.538 SAM.4: 15 residues within 4Å: Chain C: R.439, G.442 Chain D: A.421, L.423, G.442, F.443, D.444, Q.445, A.446, P.447, V.533, V.534, T.535, I.537, D.538 11 PLIP interactions: 1 interactions with chain C, 10 interactions with chain D Hydrogen bonds: C:R.439, D:L.423, D:L.423, D:Q.445, D:T.535, D:T.535, D:T.535, D:D.538 pi-Stacking: D:F.443, D:F.443 pi-Cation interactions: D:F.443 SAM.5: 15 residues within 4Å: Chain E: A.421, L.423, G.442, F.443, D.444, Q.445, A.446, P.447, V.533, T.535, D.538 Chain F: R.439, G.442, D.444 Ligands: SAM.6 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:L.423, E:D.444, E:Q.445, E:Q.445, E:T.535, E:T.535, E:D.538, F:D.444 SAM.6: 20 residues within 4Å: Chain E: R.439, G.442, F.443, D.444 Chain F: S.420, A.421, L.423, K.441, G.442, F.443, D.444, Q.445, A.446, P.447, V.533, V.534, T.535, I.537, D.538 Ligands: SAM.5 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:S.420, F:L.423, F:L.423, F:Q.445, F:D.538, E:R.439, E:F.443 pi-Stacking: F:F.443, F:F.443 SAM.7: 17 residues within 4Å: Chain G: S.420, A.421, P.422, L.423, G.442, F.443, D.444, Q.445, A.446, P.447, V.533, T.535, I.537, D.538 Chain H: G.442, L.461 Ligands: SAM.8 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:T.535, G:I.537 Hydrogen bonds: G:S.420, G:L.423, G:D.444, G:Q.445, G:Q.445, G:Q.445, G:Q.445, G:Q.445, G:D.538 pi-Stacking: G:F.443, G:F.443 SAM.8: 14 residues within 4Å: Chain G: R.439, G.442 Chain H: A.421, L.423, G.442, F.443, D.444, Q.445, A.446, P.447, V.533, T.535, D.538 Ligands: SAM.7 8 PLIP interactions: 7 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:L.423, H:Q.445, H:Q.445, H:T.535, H:D.538, G:F.443 pi-Stacking: H:F.443, H:F.443 SAM.9: 17 residues within 4Å: Chain I: S.420, A.421, P.422, L.423, G.442, F.443, D.444, Q.445, A.446, P.447, V.533, T.535, I.537, D.538 Chain J: R.439, G.442, F.443 12 PLIP interactions: 10 interactions with chain I, 2 interactions with chain J Hydrogen bonds: I:S.420, I:S.420, I:L.423, I:D.444, I:Q.445, I:Q.445, I:T.535, I:D.538, J:G.442 pi-Stacking: I:F.443, I:F.443 Hydrophobic interactions: J:R.439 SAM.10: 15 residues within 4Å: Chain I: R.439, G.442, D.444 Chain J: S.420, A.421, L.423, G.442, F.443, D.444, Q.445, P.447, V.533, T.535, I.537, D.538 8 PLIP interactions: 8 interactions with chain J Hydrophobic interactions: J:I.537 Hydrogen bonds: J:L.423, J:D.444, J:Q.445, J:Q.445, J:D.538 pi-Stacking: J:F.443, J:F.443

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCorvie, T.J. et al., Architecture and regulation of filamentous human cystathionine beta-synthase. Nat Commun (2024)

Release Date

2024-04-17

Peptides

Cystathionine beta-synthase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Cystathionine beta-synthase

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