2WDB: Hyaluronoglucosaminidase

A family 32 carbohydrate-binding module, from the Mu toxin produced by Clostridium perfringens, in complex with beta-D-glcNAc-beta(1,2) mannose. Determined by X-ray diffraction at 2.03 Å resolution. Released 5 May 2009.

Method: X-ray diffraction
Resolution: 2.03 Å
Organism: CLOSTRIDIUM PERFRINGENS
Chains: 4
Atoms: 5,090
Mol. weight: 87.28 kDa
Ligands: CA
Released: 5 May 2009

Explore 2WDB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2WDB contains 15 α-helices and 44 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	809-812	4	1
β-strand	817-821	5	1
α-helix	823-826	4
β-strand	835-838	4	1
α-helix	839	1
α-helix	840-843	4
β-strand	845	1	2
β-strand	850-868	19	1
β-strand	881-887	7	1
β-strand	894-900	7	1
α-helix	904-905	2
β-strand	909-928	20	1
β-strand	932	1	2
β-strand	936-944	9	1

Chain B: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	806	1	3
β-strand	809-812	4	4
β-strand	813	1	5
β-strand	817-821	5	4
α-helix	823-826	4
β-strand	835-838	4	4
α-helix	839	1
α-helix	840-843	4
β-strand	845	1	6
β-strand	850-868	19	4
β-strand	881-887	7	4
β-strand	893-900	8	4
α-helix	904-905	2
β-strand	909-928	20	4
β-strand	932	1	6
β-strand	936-944	9	4

Chain C: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	809-812	4	7
β-strand	817-820	4	7
α-helix	823-826	4
β-strand	835-838	4	7
α-helix	840-843	4
β-strand	845	1	8
α-helix	846	1
β-strand	850-868	19	7
β-strand	881-887	7	7
β-strand	894-900	7	7
α-helix	904-905	2
β-strand	909-928	20	7
β-strand	932	1	8
β-strand	936-944	9	7

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	806	1	5
β-strand	809-812	4	9
β-strand	813	1	3
β-strand	817-821	5	9
α-helix	823-826	4
β-strand	835-838	4	9
α-helix	839	1
β-strand	845	1	10
β-strand	850-868	19	9
β-strand	881-887	7	9
β-strand	894-900	7	9
α-helix	904-905	2
β-strand	909-928	20	9
β-strand	932	1	10
β-strand	936-944	9	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hyaluronoglucosaminidase	A, B, C, D	protein	192	CLOSTRIDIUM PERFRINGENS	P26831 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>2WDB_1 HYALURONOGLUCOSAMINIDASE (chains A, B, C, D)
MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGD
TSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTG
APAGKDVIEESFETPISAKYIRLTNMENINKWLTFSEFAIVSDELENAGNKENVYTNTEL
DLLSLAKEDVTK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4

Primary citation

N-Acetylglucosamine Recognition by a Family 32 Carbohydrate-Binding Module from Clostridium Perfringens Nagh. Ficko-Blean, E., Boraston, A.B. J Mol Biol (2009) 390:208. DOI 10.1016/J.JMB.2009.04.066 · PubMed

Other PDB entries of the same protein (UniProt P26831 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2W1S 1.45 Å, Unique ligand binding specificity of a family 32 Carbohydrate-Binding Module from the Mu…
2OZN 1.6 Å, The Cohesin-Dockerin Complex of NagJ and NagH from Clostridium perfringens
2W1Q 1.6 Å, Unique ligand binding specificity for a family 32 Carbohydrate- Binding Module from the…
2W1U 2.0 Å, A family 32 carbohydrate-binding module, from the Mu toxin produced by Clostridium…
7RGA 2.9 Å, Crystal structure of nanoCLAMP3:VHH in complex with MTX
2JNK Solution structure of a dockerin-containing modular pair from a family 84 glycoside…

Browse structure collections

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