eF-site ID 2dva-D
PDB Code 2dva
Chain D

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Title Crystal structure of peanut lectin GAL-BETA-1,3-GALNAC-ALPHA-O-ME (Methyl-T-antigen) complex
Classification SUGAR BINDING PROTEIN
Compound Galactose-binding lectin
Source ORGANISM_COMMON: peanut; ORGANISM_SCIENTIFIC: Arachis hypogaea;
Sequence D:  AETVSFNFNSFSEGNPAINFQGDVTVLSNGNIQLTNLNKV
NSVGRVLYAMPVRIWSSATGNVASFLTSFSFEMKDIKDYD
PADGIIFFIAPEDTQIPAGSIGGGTLGVSDTKGAGHFVGV
EFDTYSNSEYNDPPTDHVGIDVNSVDSVKTVPWNSVSGAV
VKVTVIYDSSTKTLSVAVTNDNGDITTIAQVVDLKAKLPE
RVKFGFSASGSLGGRQIHLIRSWSFTSTLITT
Description (1)  Galactose-binding lectin


Functional site

1) chain D
residue 80
type
ligand
sequence D
description BINDING SITE FOR RESIDUE GAL D 239
source : AC7

2) chain D
residue 82
type
ligand
sequence A
description BINDING SITE FOR RESIDUE GAL D 239
source : AC7

3) chain D
residue 83
type
ligand
sequence D
description BINDING SITE FOR RESIDUE GAL D 239
source : AC7

4) chain D
residue 103
type
ligand
sequence G
description BINDING SITE FOR RESIDUE GAL D 239
source : AC7

5) chain D
residue 104
type
ligand
sequence G
description BINDING SITE FOR RESIDUE GAL D 239
source : AC7

6) chain D
residue 125
type
ligand
sequence Y
description BINDING SITE FOR RESIDUE GAL D 239
source : AC7

7) chain D
residue 127
type
ligand
sequence N
description BINDING SITE FOR RESIDUE GAL D 239
source : AC7

8) chain D
residue 211
type
ligand
sequence S
description BINDING SITE FOR RESIDUE GAL D 239
source : AC7

9) chain D
residue 211
type
ligand
sequence S
description BINDING SITE FOR RESIDUE MGC D 240
source : AC8

10) chain D
residue 212
type
ligand
sequence L
description BINDING SITE FOR RESIDUE MGC D 240
source : AC8

11) chain D
residue 213
type
ligand
sequence G
description BINDING SITE FOR RESIDUE MGC D 240
source : AC8

12) chain D
residue 123
type
ligand
sequence D
description BINDING SITE FOR RESIDUE CA D 237
source : BC6

13) chain D
residue 125
type
ligand
sequence Y
description BINDING SITE FOR RESIDUE CA D 237
source : BC6

14) chain D
residue 127
type
ligand
sequence N
description BINDING SITE FOR RESIDUE CA D 237
source : BC6

15) chain D
residue 132
type
ligand
sequence D
description BINDING SITE FOR RESIDUE CA D 237
source : BC6

16) chain D
residue 121
type
ligand
sequence E
description BINDING SITE FOR RESIDUE MN D 238
source : BC7

17) chain D
residue 123
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MN D 238
source : BC7

18) chain D
residue 132
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MN D 238
source : BC7

19) chain D
residue 137
type
ligand
sequence H
description BINDING SITE FOR RESIDUE MN D 238
source : BC7

20) chain D
residue 123
type METAL
ligand
sequence D
description Calcium
source Swiss-Prot : SWS_FT_FI10

21) chain D
residue 127
type METAL
ligand
sequence N
description Calcium
source Swiss-Prot : SWS_FT_FI10

22) chain D
residue 132
type METAL
ligand
sequence D
description Calcium
source Swiss-Prot : SWS_FT_FI10

23) chain D
residue 121
type METAL
ligand
sequence E
description Manganese
source Swiss-Prot : SWS_FT_FI11

24) chain D
residue 123
type METAL
ligand
sequence D
description Manganese
source Swiss-Prot : SWS_FT_FI11

25) chain D
residue 132
type METAL
ligand
sequence D
description Manganese
source Swiss-Prot : SWS_FT_FI11

26) chain D
residue 137
type METAL
ligand
sequence H
description Manganese
source Swiss-Prot : SWS_FT_FI11

27) chain D
residue 125
type METAL
ligand
sequence Y
description Calcium; via carbonyl oxygen
source Swiss-Prot : SWS_FT_FI12

28) chain D
residue 118-124
type prosite
ligand
sequence VGVEFDT
description Legume lectins beta-chain signature. [LIV]-[STAG]-V-[DEQV]-[FLI]-D-[ST]
source prosite : PS00307

29) chain D
residue 198-207
type prosite
ligand
sequence LPERVKFGFS
description Legume lectins alpha-chain signature. [LIV]-{LA}-[EDQ]-[FYWKR]-V-{VF}-[LIVF]-G-[LF]-[ST]
source prosite : PS00308

30) chain D
residue 41
type binding
ligand MGC: ALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE
sequence N
description ALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE binding site
source pdb_hetatom : MGC_2dva_D_240

31) chain D
residue 101
type binding
ligand MGC: ALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE
sequence I
description ALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE binding site
source pdb_hetatom : MGC_2dva_D_240

32) chain D
residue 211-214
type binding
ligand MGC: ALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE
sequence SLGG
description ALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE binding site
source pdb_hetatom : MGC_2dva_D_240

33) chain D
residue 80
type binding
ligand GAL: BETA-D-GALACTOSE
sequence D
description BETA-D-GALACTOSE binding site
source pdb_hetatom : GAL_2dva_D_239

34) chain D
residue 82-83
type binding
ligand GAL: BETA-D-GALACTOSE
sequence AD
description BETA-D-GALACTOSE binding site
source pdb_hetatom : GAL_2dva_D_239

35) chain D
residue 103-104
type binding
ligand GAL: BETA-D-GALACTOSE
sequence GG
description BETA-D-GALACTOSE binding site
source pdb_hetatom : GAL_2dva_D_239

36) chain D
residue 125
type binding
ligand GAL: BETA-D-GALACTOSE
sequence Y
description BETA-D-GALACTOSE binding site
source pdb_hetatom : GAL_2dva_D_239

37) chain D
residue 127
type binding
ligand GAL: BETA-D-GALACTOSE
sequence N
description BETA-D-GALACTOSE binding site
source pdb_hetatom : GAL_2dva_D_239

38) chain D
residue 129
type binding
ligand GAL: BETA-D-GALACTOSE
sequence E
description BETA-D-GALACTOSE binding site
source pdb_hetatom : GAL_2dva_D_239

39) chain D
residue 210-211
type binding
ligand GAL: BETA-D-GALACTOSE
sequence GS
description BETA-D-GALACTOSE binding site
source pdb_hetatom : GAL_2dva_D_239

40) chain D
residue 213-214
type binding
ligand GAL: BETA-D-GALACTOSE
sequence GG
description BETA-D-GALACTOSE binding site
source pdb_hetatom : GAL_2dva_D_239


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