MolNFT v1 · #70125 · protein

Crystal structure of the B. circulans CPA123 circular permutant

3LB9 · Endo-1,4-beta-xylanase: “Crystal structure of the B. circulans CPA123 circular permutant”. X-ray diffraction, 4 pockets (best druggability 0.70). MolNFT v1 #70125 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3LB9
Type: protein
Length: 546 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endo-1,4-beta-xylanase
EC: 3.2.1.8
UniProt: P09850
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 62% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Endo-1,4-beta-xylanase (EC 3.2.1.8)	protein	182	5% helix, 62% strand	P09850

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	665	0.70	0.78	64	empty
2	662	0.66	0.75	63	empty
3	91	0.38	0.77	24	empty
4	112	0.37	0.74	20	empty

Interfaces

3 interfaces between chains.

A–B · 596 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 336 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 17 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3LB9 · Crystal structure of the B. circulans cpA123 circular permutant · the same entry in another collection · chain A against A, TM-score 1.00
P09850 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase (P09850) · a predicted model of the same protein · chain A against A, TM-score 0.64

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 P09850
Elsewhere: RCSB PDB 3LB9 · PDBe 3LB9 · UniProt P09850

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