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2.85 a crystal structure of pedf

Analyse 2.85 a crystal structure of pedf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IMV
Type: protein
Length: 375 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pigment epithelium-derived factor
UniProt: P36955
Ligands: NAG
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pigment epithelium-derived factor	protein	375	33% helix, 31% strand	P36955

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A

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

Pockets

4 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	51	0.51	0.88	18	empty
2	124	0.44	0.77	25	empty
3	71	0.36	0.77	15	empty
4	55	0.31	0.76	16	empty

Modifications

Observed in the structure: 1 glycan (N-glycosylation).

Compared structures

1IMV · 2.85 A crystal structure of PEDF · the same entry in another collection · chain A against A, TM-score 1.00
P36955 · AlphaFold monomer V2.0 prediction for pigment epithelium-derived factor (P36955) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P36955
Elsewhere: RCSB PDB 1IMV · PDBe 1IMV · UniProt P36955

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