SMTL ID : 4l8w.1 (3 other biounits)

Crystal structure of gamma glutamyl hydrolase (H218N) from zebrafish complex with MTX polyglutamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-hexamer

Ligands

2 x MTX: METHOTREXATE(Non-covalent)

MTX.1: 14 residues within 4Å: Chain B: F.41, G.92, G.93, G.94, V.95, C.129, L.130, E.133, S.189, H.190, Q.191, W.192 Ligands: DGL.2, DGL.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.93, B:L.130, B:E.133, B:Q.191, B:W.192 pi-Stacking: B:F.41 MTX.4: 14 residues within 4Å: Chain E: F.41, G.92, G.93, G.94, V.95, C.129, L.130, E.133, S.189, H.190, Q.191, W.192 Ligands: DGL.5, DGL.6 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:G.93, E:G.93, E:L.130, E:Q.191, E:W.192 pi-Stacking: E:F.41, E:F.41

4 x DGL: D-GLUTAMIC ACID(Non-covalent)

DGL.2: 10 residues within 4Å: Chain B: Y.50, G.93, G.94, C.129, S.189, N.239, K.242, F.305 Ligands: MTX.1, DGL.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.305 Hydrogen bonds: B:Y.50, B:G.93, B:S.189 Salt bridges: B:K.242 DGL.3: 6 residues within 4Å: Chain B: Y.50, S.303, A.304, F.305 Ligands: MTX.1, DGL.2 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.305 Hydrogen bonds: B:A.304 DGL.5: 10 residues within 4Å: Chain E: Y.50, G.92, G.93, G.94, C.129, S.189, N.239, K.242 Ligands: MTX.4, DGL.6 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Y.50, E:G.93, E:S.189 Water bridges: E:G.94 Salt bridges: E:K.242 DGL.6: 6 residues within 4Å: Chain E: Y.50, S.303, A.304, F.305 Ligands: MTX.4, DGL.5 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.305 Hydrogen bonds: E:A.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chuankhayan, P. et al., Structural insights into the hydrolysis and polymorphism of methotrexate polyglutamate by zebrafish gamma-glutamyl hydrolase. J.Med.Chem. (2013)

Release Date

2014-05-14

Peptides

Gamma-glutamyl hydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
I

C
B

D
E

E
G

F
K

Gamma-glutamyl hydrolase

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