eF-site ID 2zxq-A
PDB Code 2zxq
Chain A

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Title Crystal structure of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum (EngBF)
Classification HYDROLASE
Compound Endo-alpha-N-acetylgalactosaminidase
Source Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b) (Q3T552_BIFLO)
Sequence A:  ASETLKTKKMEVQIKKNFPSVLQYTMTDGKVMYGQSKDVR
TVEINGTNIELGDDDVTFKKVSDTEATYTLKVKDEAKKID
AVITVQITVKANQLHLNVTKIKNNLSEGIPEGNGVEENAI
QTLSFPNQSLVSVRSSQENAQFTGARMSSNTQKPGDTNFA
VTEDTNVTDSDYTYGFISGAGLSAGLWSNSEHDGTYVAAP
VRGGSQNTRVYATTQQTGDATSLGLASAPWYYHRTVTDSK
GKKYTVAETALPQMAVAIAGDENEDGAVNWQDGAIAYRDI
MNNPYKSEEVPELVAWRIAMNFGSQAQNPFLTTLDNVKKV
ALNTDGLGQSVLLKGYGNEGHDSGHPDYGDIGQRLGGADD
MNTMMEEGSKYGARFGVHVNASEMYPEAKAFSEDMVRRNS
AGGLSYGWNWLDQGVGIDGIYDLASGSRVSRFADLSKEVG
DNMDFIYLDVWGNLTSSGSEDSWETRKMSKMINDNGWRMT
TEWGSGNEYDSTFQHWAADLTYGGYTSKGENSEVMRFLRN
HQKDSWVGDYPQYGGAANAPLLGGYNMKDFEGWQGRNDYA
AYIKNLYTHDVSTKFIQHFKVTRWVNNPLLTADNGNAAAV
SDPNTNNGNEQITLKDSNGNVVVVSRGSNDTSSAAYRQRT
ITFNGVKVASGVVSAGDGSATGDESYLLPWMWDSFTGKLV
KDSEQKLYHWNTKGGTTTWTLPDSWKNLSSVKVYQLTDQG
KTNEQTVAVSGGKVTLTADAETPYVVYKGEAKQIQVNWSE
GMHVVDAGFNGGSNTLTDNWTVSGSGKAEVEGDNNAMLRL
TGKVDVSQRLTDLKAGQKYALYVGVDNRSTGDASVTVTSG
GKVLATNSTGKSIAKNYIKAYGHNTNSNTENGSSYFQNMY
VFFTAPENGDATVTLSHKSTDGAHTYFDDVRIVENQYSGI
TYEKDGTLKSLTNGFENNAQGIWPFVVSGSEGVEDNRIHL
SELHAPFTRAGWDVKKMDDVLDGTWSVKVNGLTQKGTLVY
QTIPQNVKFEAGAKYKVSFDYQSGSDDIYAIAVGQGEYSA
GSVKLTNLKKALGETGKAEFELTGGVNGDSWFGIYSTATA
PDLQGSTGNAQDFGGYKDFVLDNLKIERIESQTRTKAEAQ
DKVKEIRGKYDSKRAWQQYQDTLVKARVLINKNGATAEDF
TKAYDILVALDEYMKTAP
Description (1)  Endo-alpha-N-acetylgalactosaminidase (E.C.3.2.1.97)


Functional site

1) chain A
residue 601
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MN A 1
source : AC1

2) chain A
residue 603
type
ligand
sequence N
description BINDING SITE FOR RESIDUE MN A 1
source : AC1

3) chain A
residue 605
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MN A 1
source : AC1

4) chain A
residue 607
type
ligand
sequence A
description BINDING SITE FOR RESIDUE MN A 1
source : AC1

5) chain A
residue 612
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MN A 1
source : AC1

6) chain A
residue 727
type
ligand
sequence E
description BINDING SITE FOR RESIDUE MN A 2
source : AC2

7) chain A
residue 752
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MN A 2
source : AC2

8) chain A
residue 1299
type
ligand
sequence H
description BINDING SITE FOR RESIDUE MN A 2
source : AC2

9) chain A
residue 1108
type
ligand
sequence G
description BINDING SITE FOR RESIDUE MN A 3
source : AC3

10) chain A
residue 1135
type
ligand
sequence N
description BINDING SITE FOR RESIDUE MN A 3
source : AC3

11) chain A
residue 1136
type
ligand
sequence A
description BINDING SITE FOR RESIDUE MN A 3
source : AC3

12) chain A
residue 1248
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MN A 3
source : AC3

13) chain A
residue 1274
type
ligand
sequence G
description BINDING SITE FOR RESIDUE MN A 4
source : AC4

14) chain A
residue 1276
type
ligand
sequence E
description BINDING SITE FOR RESIDUE MN A 4
source : AC4

15) chain A
residue 1322
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MN A 4
source : AC4

16) chain A
residue 1325
type
ligand
sequence W
description BINDING SITE FOR RESIDUE MN A 4
source : AC4

17) chain A
residue 1442
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MN A 4
source : AC4

18) chain A
residue 1273
type
ligand
sequence N
description BINDING SITE FOR RESIDUE MPD A1695
source : AC5

19) chain A
residue 1274
type
ligand
sequence G
description BINDING SITE FOR RESIDUE MPD A1695
source : AC5

20) chain A
residue 1275
type
ligand
sequence F
description BINDING SITE FOR RESIDUE MPD A1695
source : AC5

21) chain A
residue 1276
type
ligand
sequence E
description BINDING SITE FOR RESIDUE MPD A1695
source : AC5

22) chain A
residue 1277
type
ligand
sequence N
description BINDING SITE FOR RESIDUE MPD A1695
source : AC5

23) chain A
residue 541
type
ligand
sequence V
description BINDING SITE FOR RESIDUE MPD A1696
source : AC6

24) chain A
residue 823
type
ligand
sequence W
description BINDING SITE FOR RESIDUE MPD A1696
source : AC6

25) chain A
residue 874
type
ligand
sequence G
description BINDING SITE FOR RESIDUE MPD A1697
source : AC7

26) chain A
residue 875
type
ligand
sequence G
description BINDING SITE FOR RESIDUE MPD A1697
source : AC7

27) chain A
residue 878
type
ligand
sequence N
description BINDING SITE FOR RESIDUE MPD A1697
source : AC7

28) chain A
residue 971
type
ligand
sequence T
description BINDING SITE FOR RESIDUE MPD A1697
source : AC7

29) chain A
residue 981
type METAL
ligand
sequence I
description Manganese; via tele nitrogen
source Swiss-Prot : SWS_FT_FI1

30) chain A
residue 409
type METAL
ligand
sequence T
description Manganese
source Swiss-Prot : SWS_FT_FI2

31) chain A
residue 434
type METAL
ligand
sequence L
description Manganese
source Swiss-Prot : SWS_FT_FI2

32) chain A
residue 966-979
type prosite
ligand
sequence RGSNDTSSAAYRQR
description Basic-leucine zipper (bZIP) domain signature. [KR]-x(1,3)-[RKSAQ]-N-{VL}-x-[SAQ](2)-{L}-[RKTAENQ]-x-R-{S}-[RK]
source prosite : PS00036

33) chain A
residue 540-541
type binding
ligand MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
sequence PV
description (4S)-2-METHYL-2,4-PENTANEDIOL binding site
source pdb_hetatom : MPD_2zxq_A_1696

34) chain A
residue 793
type binding
ligand MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
sequence N
description (4S)-2-METHYL-2,4-PENTANEDIOL binding site
source pdb_hetatom : MPD_2zxq_A_1696

35) chain A
residue 823
type binding
ligand MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
sequence W
description (4S)-2-METHYL-2,4-PENTANEDIOL binding site
source pdb_hetatom : MPD_2zxq_A_1696

36) chain A
residue 836
type binding
ligand MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
sequence W
description (4S)-2-METHYL-2,4-PENTANEDIOL binding site
source pdb_hetatom : MPD_2zxq_A_1696

37) chain A
residue 871
type binding
ligand MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
sequence P
description (4S)-2-METHYL-2,4-PENTANEDIOL binding site
source pdb_hetatom : MPD_2zxq_A_1697

38) chain A
residue 874-875
type binding
ligand MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
sequence GG
description (4S)-2-METHYL-2,4-PENTANEDIOL binding site
source pdb_hetatom : MPD_2zxq_A_1697

39) chain A
residue 878
type binding
ligand MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
sequence N
description (4S)-2-METHYL-2,4-PENTANEDIOL binding site
source pdb_hetatom : MPD_2zxq_A_1697

40) chain A
residue 971
type binding
ligand MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
sequence T
description (4S)-2-METHYL-2,4-PENTANEDIOL binding site
source pdb_hetatom : MPD_2zxq_A_1697

41) chain A
residue 976
type binding
ligand MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
sequence Y
description (4S)-2-METHYL-2,4-PENTANEDIOL binding site
source pdb_hetatom : MPD_2zxq_A_1697

42) chain A
residue 1257
type binding
ligand MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
sequence Y
description (4S)-2-METHYL-2,4-PENTANEDIOL binding site
source pdb_hetatom : MPD_2zxq_A_1695

43) chain A
residue 1272-1277
type binding
ligand MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
sequence TNGFEN
description (4S)-2-METHYL-2,4-PENTANEDIOL binding site
source pdb_hetatom : MPD_2zxq_A_1695


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