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Crystal structure of CBM31 from beta-1,3-xylanase

Analyse Crystal structure of CBM31 from beta-1,3-xylanase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2COV
Type: protein
Length: 534 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-1,3-xylanase
UniProt: Q8RS40
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 2% helix, 60% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, E	Beta-1,3-xylanase	protein	92	3% helix, 58% strand	Q8RS40
F, H	Beta-1,3-xylanase	protein	87	0% helix, 61% strand	Q8RS40
G	Beta-1,3-xylanase	protein	88	3% helix, 60% strand	Q8RS40
I	Beta-1,3-xylanase	protein	88	0% helix, 60% strand	Q8RS40

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	891	0.84	0.85	94	empty
2	549	0.75	0.82	35	empty
3	541	0.75	0.82	35	empty
4	197	0.48	0.75	26	empty
5	171	0.47	0.76	28	empty

Interfaces

12 interfaces between chains.

D–E · 593 Å² buried · 18 hydrogen bonds · protein-protein
H–I · 585 Å² buried · 21 hydrogen bonds · protein-protein
F–G · 580 Å² buried · 20 hydrogen bonds · protein-protein
D–G · 346 Å² buried · 2 hydrogen bonds · protein-protein
E–H · 340 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

2COV · Crystal structure of CBM31 from beta-1,3-xylanase · the same entry in another collection · chain I against I, TM-score 1.00
Q8RS40 · AlphaFold monomer V2.0 prediction for beta-1,3-xylanase (Q8RS40) · a predicted model of the same protein · chain I against A, TM-score 0.95

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8RS40
Elsewhere: RCSB PDB 2COV · PDBe 2COV · UniProt Q8RS40

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