MolNFT v1 · #142824 · protein

Acetyl xylan esterase from paenibacillus sp. R4

6AGQ: “Acetyl xylan esterase from paenibacillus sp. R4”. X-ray diffraction, 1 ligand (ZN), 19 pockets (best druggability 0.82). MolNFT v1 #142824 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6AGQ
Type: protein
Length: 1,896 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetyl xylan esterase
Ligands: ZN
Pockets: 19 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Acetyl xylan esterase	protein	316	35% helix, 20% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	154	0.82	0.98	32	empty
2	159	0.81	0.97	29	empty
3	150	0.80	0.97	32	empty
4	821	0.76	0.80	90	empty
5	1165	0.73	0.76	84	empty

Interfaces

12 interfaces between chains.

D–E · 959 Å² buried · 29 hydrogen bonds · protein-protein
C–F · 945 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 943 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 929 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 912 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6AGQ · Acetyl xylan esterase from Paenibacillus sp. R4 · 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
Elsewhere: RCSB PDB 6AGQ · PDBe 6AGQ

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