SMTL ID : 3cog.1

Crystal structure of human cystathionase (Cystathionine gamma lyase) in complex with DL-propargylglycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 10 residues within 4Å: Chain A: Y.115, N.162, K.213, E.340, S.341, L.342, T.356, R.376 Ligands: PLP.2, 2AG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.162, A:K.213, A:K.213, A:S.341, A:R.376, A:R.376 NO3.6: 10 residues within 4Å: Chain C: Y.115, N.162, K.213, E.340, S.341, L.342, T.356, R.376 Ligands: PLP.7, 2AG.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.162, C:S.341, C:S.341, C:R.376, C:R.376 NO3.10: 10 residues within 4Å: Chain D: Y.115, N.162, K.213, E.340, S.341, L.342, T.356, R.376 Ligands: PLP.11, 2AG.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.162, D:S.341, D:T.356, D:R.376, D:R.376

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

PLP.2: 17 residues within 4Å: Chain A: S.90, G.91, L.92, Y.115, E.158, N.162, D.188, T.190, S.210, T.212, K.213, V.222, M.223, L.342 Chain B: Y.61, R.63 Ligands: NO3.1 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A Salt bridges: B:R.63, A:K.213 Hydrophobic interactions: A:Y.115, A:T.190, A:K.213 Hydrogen bonds: A:G.91, A:L.92, A:N.162, A:T.190, A:S.210, A:S.210 Water bridges: A:E.158 PLP.7: 16 residues within 4Å: Chain C: S.90, G.91, L.92, Y.115, E.158, N.162, D.188, T.190, S.210, T.212, K.213, M.223, L.342 Chain D: Y.61, R.63 Ligands: NO3.6 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:T.190, C:K.213 Hydrogen bonds: C:G.91, C:L.92, C:N.162, C:S.210, C:S.210, C:T.212, C:K.213, D:Y.61 Water bridges: C:T.118 Salt bridges: C:K.213, D:R.63 pi-Stacking: C:Y.115 PLP.11: 17 residues within 4Å: Chain C: Y.61, R.63 Chain D: S.90, G.91, L.92, Y.115, E.158, N.162, D.188, T.190, S.210, T.212, K.213, M.223, L.342 Ligands: NO3.10, 2AG.12 13 PLIP interactions: 2 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:Y.61, D:G.91, D:L.92, D:N.162, D:S.210, D:S.210, D:T.212 Salt bridges: C:R.63, D:K.213 Hydrophobic interactions: D:T.190, D:K.213 Water bridges: D:T.118 pi-Stacking: D:Y.115

3 x 2AG: (2S)-2-aminopent-4-enoic acid(Covalent)

2AG.3: 7 residues within 4Å: Chain A: Y.115, R.120, E.340 Chain B: Y.61, R.63, N.242 Ligands: NO3.1 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.61, B:Y.61, A:Y.115 Hydrogen bonds: B:N.242, A:E.340 Water bridges: B:S.64, A:T.356, A:S.359 Salt bridges: B:R.63, A:R.120 2AG.8: 7 residues within 4Å: Chain C: Y.115, R.120, E.340 Chain D: Y.61, R.63, N.242 Ligands: NO3.6 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:Y.115, D:Y.61, D:Y.61 Hydrogen bonds: C:E.340, D:N.242 Water bridges: C:R.120, C:R.120, C:S.359, D:S.64, D:S.64 Salt bridges: C:R.120, D:R.63 2AG.12: 9 residues within 4Å: Chain C: E.60, Y.61, R.63, N.242 Chain D: Y.115, R.120, E.340 Ligands: NO3.10, PLP.11 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:Y.61, D:Y.115 Hydrogen bonds: C:N.242, D:E.340 Water bridges: C:S.64, C:N.242, D:R.120, D:T.356, D:S.359 Salt bridges: C:R.63, D:R.120

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: H.100, L.101, L.102, L.240 Chain B: Q.124, V.125, E.128, F.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.100 Water bridges: A:R.236, A:R.236 GOL.9: 6 residues within 4Å: Chain C: H.100, L.101, L.102, L.240 Chain D: V.125, E.128 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.100 Water bridges: C:R.236, C:R.236 GOL.13: 7 residues within 4Å: Chain C: V.125, E.128, F.129 Chain D: H.100, L.101, L.102, K.103 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.103 Water bridges: D:L.101, D:L.101, D:R.236, D:R.236 GOL.14: 6 residues within 4Å: Chain B: W.33, T.34, S.35 Chain D: W.33, T.34, S.35 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:T.34, B:T.34, B:S.35, B:S.35, D:T.34, D:S.35, D:S.35 Water bridges: B:T.34 GOL.15: 8 residues within 4Å: Chain C: L.44, S.249, P.250 Chain D: D.220, V.221, V.222, D.252, L.255 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.222, D:V.222, D:D.252

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 8 residues within 4Å: Chain A: P.296, H.298, P.299, Q.300, H.301, E.302, L.303, R.306 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.302, A:L.303, A:R.306, A:R.306 Water bridges: A:S.297, A:H.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Q. et al., Structural basis for the inhibition mechanism of human cystathionine gamma-lyase, an enzyme responsible for the production of H(2)S. J.Biol.Chem. (2009)

Release Date

2008-05-27

Peptides

Cystathionine gamma-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cystathionine gamma-lyase

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