SMTL ID : 1pff.1

Crystal Structure of Homocysteine alpha-, gamma-lyase at 1.8 Angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: G.37, E.64, N.83 Ligands: PEG.18 Ligand excluded by PLIP EDO.2: 2 residues within 4Å: Chain A: S.1, A.2 Ligand excluded by PLIP EDO.3: 1 residues within 4Å: Ligands: EDO.8 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: F.67, H.79 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: H.215, K.221, K.222 Ligands: EDO.6, EDO.7 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: H.215, E.216, K.218 Ligands: EDO.5, EDO.7 Ligand excluded by PLIP EDO.7: 10 residues within 4Å: Chain A: L.214, H.215, E.216, H.217, K.218, V.220, K.221, V.223 Ligands: EDO.5, EDO.6 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: P.82 Ligands: EDO.3, PEG.18 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: T.32, K.167, Q.171 Ligands: EDO.11 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: L.10, I.127, D.197 Chain D: E.314, N.315, D.318 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: K.167 Ligands: EDO.9, EDO.12 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: F.33, R.161, D.163, K.167 Ligands: EDO.11 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: R.59, E.64, V.65 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain A: K.111 Ligand excluded by PLIP EDO.15: 1 residues within 4Å: Chain A: K.111 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: I.26, Y.47, D.120, S.142 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: A.271, V.272, S.273 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: D.44, C.45, N.94, P.95, T.96, A.300, G.301 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain B: H.215, E.216 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: L.10, H.12, P.126, N.130 Ligand excluded by PLIP EDO.22: 1 residues within 4Å: Chain B: D.133 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: G.37, E.64, N.83 Ligands: PEG.42 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain C: S.1, A.2 Ligand excluded by PLIP EDO.27: 1 residues within 4Å: Ligands: EDO.32 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain C: F.67, H.79 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain C: H.215, K.221, K.222 Ligands: EDO.30, EDO.31 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain C: H.215, E.216, K.218 Ligands: EDO.29, EDO.31 Ligand excluded by PLIP EDO.31: 10 residues within 4Å: Chain C: L.214, H.215, E.216, H.217, K.218, V.220, K.221, V.223 Ligands: EDO.29, EDO.30 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain C: P.82 Ligands: EDO.27, PEG.42 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain C: T.32, K.167, Q.171 Ligands: EDO.35 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain B: E.314, N.315, D.318 Chain C: L.10, I.127, D.197 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain C: K.167 Ligands: EDO.33, EDO.36 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain C: F.33, R.161, D.163, K.167 Ligands: EDO.35 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain C: R.59, E.64, V.65 Ligand excluded by PLIP EDO.38: 1 residues within 4Å: Chain C: K.111 Ligand excluded by PLIP EDO.39: 1 residues within 4Å: Chain C: K.111 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain C: I.26, Y.47, D.120, S.142 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain C: A.271, V.272, S.273 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain D: D.44, C.45, N.94, P.95, T.96, A.300, G.301 Ligand excluded by PLIP EDO.44: 2 residues within 4Å: Chain D: H.215, E.216 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain D: L.10, H.12, P.126, N.130 Ligand excluded by PLIP EDO.46: 1 residues within 4Å: Chain D: D.133 Ligand excluded by PLIP

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

PEG.18: 4 residues within 4Å: Chain A: N.83, R.85 Ligands: EDO.1, EDO.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.85 PEG.23: 6 residues within 4Å: Chain B: L.128, K.238, K.239, Q.240, M.241, K.242 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.128, B:K.242 Water bridges: B:N.130 PEG.24: 12 residues within 4Å: Chain A: A.20, V.154, I.180, I.181, S.182, P.183 Chain B: A.20, V.154, I.180, I.181, S.182, D.185 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:V.154, A:V.154 Water bridges: B:S.182, A:S.182, A:D.185 PEG.42: 4 residues within 4Å: Chain C: N.83, R.85 Ligands: EDO.25, EDO.32 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.85 PEG.47: 6 residues within 4Å: Chain D: L.128, K.238, K.239, Q.240, M.241, K.242 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.128, D:K.242 Water bridges: D:N.130 PEG.48: 12 residues within 4Å: Chain C: A.20, V.154, I.180, I.181, S.182, P.183 Chain D: A.20, V.154, I.180, I.181, S.182, D.185 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:V.154, D:V.154, D:D.185 Water bridges: C:S.182, D:S.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

 - 

Release Date

2004-08-10

Peptides

methionine gamma-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

methionine gamma-lyase