PDB ID 1D2C     CHAIN A
Protein name PROTEIN (GLYCINE N-METHYLTRANSFERASE)
Uniprot Accession P13255
The number of similar proteins 50
The number of binding states 3
The number of binding partners 1

Coloring

Unicolor (beige)

The number of binding partners

Group

Binding
state
Binding partners
1D2C (CHAIN: A)
1 P13255  
2 P13255   P13255  
3 P13255   P13255   P13255  

Downdload

Format:

Molecule viewer


Only interaction residues
#binding
partners
  1
  0

Sequence information

1   VDSVYRTRSL   GVAAEGIPDQ   YADGEAARVW   QLYIGDTRSR   TAEYKAWLLG   50
51   LLRQHGCHRV   LDVACGTGVD   SIMLVEEGFS   VTSVDASDKM   LKYALKERWN   100
101   RRKEPAFDKW   VIEEANWLTL   DKDVPAGDGF   DAVICLGNSF   AHLPDSKGDQ   150
151   SEHRLALKNI   ASMVRPGGLL   VIDHRNYDYI   LSTGCAPPGK   NIYYKSDLTK   200
201   DITTSVLTVN   NKAHMVTLDY   TVQVPGAGRD   GAPGFSKFRL   SYYPHCLASF   250
251   TELVQEAFGG   RCQHSVLGDF   KPYRPGQAYV   PCYFIHVLKK   TG   300

Variants

Residue AA Source dbSNP Clinical
Significance
Allele
Frequency
(> 0.0001)
Disease name
29_VAL MET gnomAD
chr6:42928593
rs538620810
- 0.000149722 -
41_THR PRO 8.3kJPN
chr6:42928629
-
- 0.0019 -
49_LEU PRO ClinVar
chr6:42928654
rs121907888
Pathogenic - Glycine N-methyltransferase deficiency [MONDO:MONDO:0011698,MedGen:C1847720,OMIM:606664,Orphanet:289891]
81_VAL MET 8.3kJPN
chr6:42929987
-
- 0.0001 -
96_LYS GLU 8.3kJPN
chr6:42930032
-
- 0.0001 -
100_ASN ASP gnomAD
chr6:42930044
rs746552607
- 0.000111362 -
102_ARG TRP 8.3kJPN
chr6:42930050
rs749599022
- 0.0001 -
102_ARG GLN 8.3kJPN
chr6:42930051
rs781167464
- 0.0002 -
106_ALA THR gnomAD
chr6:42930062
rs535188125
- 0.00144861 -
109_LYS ASN 8.3kJPN
chr6:42930073
rs759573326
- 0.0001 -
123_ASP GLY 8.3kJPN
chr6:42930536
-
- 0.0001 -
124_VAL MET gnomAD
chr6:42930538
rs143043221
- 0.000373766 -
138_ASN SER ClinVar
chr6:42930587
rs864321678
Pathogenic - Glycine N-methyltransferase deficiency [MONDO:MONDO:0011698,MedGen:C1847720,OMIM:606664,Orphanet:289891]
148_GLY VAL 8.3kJPN
chr6:42930810
rs1463626619
- 0.0001 -
153_HIS PRO gnomAD
chr6:42930825
rs138085632
- 0.000136054 -
154_ARG TRP gnomAD
chr6:42930827
rs142613217
- 0.000220159 -
154_ARG GLN gnomAD
chr6:42930828
rs563826316
- 0.000128069 -
154_ARG GLN 8.3kJPN
chr6:42930828
rs563826316
- 0.0001 -
174_HIS ASN gnomAD
chr6:42930887
rs121907889
- 0.000406822 -
174_HIS ARG 8.3kJPN
chr6:42930888
rs201256313
- 0.0001 -
179_HIS PRO 8.3kJPN
chr6:42930903
rs200543916
- 0.0001 -
209_VAL GLY 8.3kJPN
chr6:42931106
-
- 0.0001 -
223_GLN ARG 8.3kJPN
chr6:42931148
-
- 0.0001 -
225_PRO LEU 8.3kJPN
chr6:42931154
rs764303705
- 0.0008 -
228_GLY ARG 8.3kJPN
chr6:42931162
-
- 0.0001 -
234_GLY SER 8.3kJPN
chr6:42931180
rs755716132
- 0.0001 -
239_ARG TRP 8.3kJPN
chr6:42931280
rs946974235
- 0.0001 -
258_PHE LEU gnomAD
chr6:42931339
rs201991849
- 0.000107377 -
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Reference

PiSite: a database of protein interaction sites using multiple binding states in the PDB, Miho Higurashi, Takashi Ishida and Kengo Kinoshita, Nucleic Acids Research 2009 37(Database issue):D360-D364

COPYRIGHTc2008-2019 Miho Higurashi, Takashi Ishida and Kengo Kinoshita. All rights reserved.