MolNFT v1 · #183301 · protein

Structure of XYN11 from pseudothermotoga thermarum

7NL2 · Beta-xylanase: “Structure of XYN11 from pseudothermotoga thermarum”. X-ray diffraction, 1 ligand (IPT), 6 pockets (best druggability 0.51). MolNFT v1 #183301 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7NL2
Type: protein
Length: 669 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-xylanase
EC: 3.2.1.8
UniProt: F7YXD6
Ligands: IPT
Pockets: 6 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-xylanase (EC 3.2.1.8)	protein	335	40% helix, 20% strand	F7YXD6
B	Beta-xylanase (EC 3.2.1.8)	protein	334	40% helix, 20% strand	F7YXD6

Ligands and binding sites

IPT · 1-methylethyl 1-thio-beta-D-galactopyranoside · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · 5 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	161	0.51	0.78	28	IPT
2	142	0.48	0.78	25	GOL, IPT
3	135	0.42	0.75	25	empty
4	91	0.37	0.76	13	empty
5	63	0.33	0.76	13	empty

Interfaces

1 interface between chains.

A–B · 694 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7NL2 · Structure of Xyn11 from Pseudothermotoga thermarum · the same entry in another collection · chain A against A, TM-score 1.00

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 F7YXD6
Elsewhere: RCSB PDB 7NL2 · PDBe 7NL2 · UniProt F7YXD6

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