MolNFT v1 · #37880 · protein

Crystal structure of the phytase from D. castellii at 2.3 a

2GFI: “Crystal structure of the phytase from D. castellii at 2.3 a”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.84). MolNFT v1 #37880 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GFI
Type: protein
Length: 916 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phytase
EC: 3.1.3.8
UniProt: A2TBB4
Ligands: NAG
Pockets: 9 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phytase (EC 3.1.3.8)	protein	458	43% helix, 13% strand	A2TBB4

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1066	0.84	0.84	86	empty
2	515	0.70	0.80	75	empty
3	144	0.62	0.85	26	empty
4	490	0.61	0.76	43	empty
5	370	0.60	0.77	56	empty

Interfaces

1 interface between chains.

A–B · 2552 Å² buried · 48 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

2GFI · Crystal structure of the phytase from D. castellii at 2.3 A · 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 A2TBB4
Elsewhere: RCSB PDB 2GFI · PDBe 2GFI · UniProt A2TBB4

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