SMTL ID : 2azt.1

Crystal structure of H176N mutant of human Glycine N-Methyltransferase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

10 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.1: 7 residues within 4Å: Chain A: G.187, C.188, A.189, P.190, V.205, T.207 Chain C: N.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.189, A:T.207 BME.2: 3 residues within 4Å: Chain A: I.283, P.284, C.285 No protein-ligand interaction detected (PLIP) BME.5: 7 residues within 4Å: Chain B: G.187, C.188, A.189, P.190, V.205, T.207 Chain D: N.213 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.189, B:A.189, B:T.207 BME.6: 2 residues within 4Å: Chain B: L.184, C.249 No protein-ligand interaction detected (PLIP) BME.7: 5 residues within 4Å: Chain B: H.182, K.193, I.283, P.284, C.285 No protein-ligand interaction detected (PLIP) BME.9: 7 residues within 4Å: Chain A: N.213 Chain C: G.187, C.188, A.189, P.190, V.205, T.207 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.189, C:T.207 BME.10: 3 residues within 4Å: Chain C: I.283, P.284, C.285 No protein-ligand interaction detected (PLIP) BME.13: 7 residues within 4Å: Chain B: N.213 Chain D: G.187, C.188, A.189, P.190, V.205, T.207 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.189, D:A.189, D:T.207 BME.14: 2 residues within 4Å: Chain D: L.184, C.249 No protein-ligand interaction detected (PLIP) BME.15: 5 residues within 4Å: Chain D: H.182, K.193, I.283, P.284, C.285 No protein-ligand interaction detected (PLIP)

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 10 residues within 4Å: Chain A: Y.34, G.140, N.141, H.145, R.178, N.194, Y.223, Y.245, Y.286 Chain B: E.16 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.141, A:Y.245 Hydrogen bonds: A:G.140, A:G.140, A:N.141, A:N.194, A:Y.245, A:Y.286 Salt bridges: A:H.145, A:R.178 CIT.8: 10 residues within 4Å: Chain A: E.16 Chain B: Y.34, G.140, N.141, H.145, N.194, Y.223, L.243, Y.245, Y.286 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.34, B:Y.245 Hydrogen bonds: B:Y.34, B:N.141, B:N.194, B:Y.223, B:Y.286 Water bridges: B:R.178 Salt bridges: B:H.145 CIT.11: 10 residues within 4Å: Chain C: Y.34, G.140, N.141, H.145, R.178, N.194, Y.223, Y.245, Y.286 Chain D: E.16 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:N.141, C:Y.245 Hydrogen bonds: C:G.140, C:G.140, C:N.141, C:N.194, C:Y.245, C:Y.286 Salt bridges: C:H.145, C:R.178 CIT.16: 10 residues within 4Å: Chain C: E.16 Chain D: Y.34, G.140, N.141, H.145, N.194, Y.223, L.243, Y.245, Y.286 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.34, D:Y.245 Hydrogen bonds: D:Y.34, D:N.141, D:N.194, D:Y.223, D:Y.286 Water bridges: D:R.178 Salt bridges: D:H.145

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain B: Q.59, F.80 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain D: Q.59, F.80 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luka, Z. et al., Destabilization of human glycine N-methyltransferase by H176N mutation. Protein Sci. (2007)

Release Date

2006-09-26

Peptides

Glycine N-methyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glycine N-methyltransferase