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Crystal structrual of a soluble protein

Analyse Crystal structrual of a soluble protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OIC
Type: protein
Length: 487 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bet V I allergen-like; Probable protein phosphatase 2C 6
EC: 3.1.3.16
UniProt: Q5Z8S0, Q0JLP9
Ligands: A8S, MN, NA, CL
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bet V I allergen-like	protein	182	31% helix, 34% strand	Q5Z8S0
B	Probable protein phosphatase 2C 6 (EC 3.1.3.16)	protein	305	33% helix, 30% strand	Q0JLP9

Ligands and binding sites

A8S · (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid · ligand · chains A
MN · Manganese (II) ion · metal · 4 copies · chains B
NA · Sodium ion · metal · chains B
CL · Chloride ion · ion · chains A, B

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

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	219	0.84	0.97	29	A8S
2	236	0.54	0.77	37	CL, MN
3	224	0.49	0.74	22	empty
4	90	0.48	0.81	20	empty

Interfaces

1 interface between chains.

A–B · 897 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4OIC · Crystal structrual of a soluble protein · the same entry in another collection · chain A against A, TM-score 1.00
Q0JLP9 · AlphaFold monomer V2.0 prediction for probable protein phosphatase 2C 6 (Q0JLP9) · a predicted model of the same protein · chain B against A, TM-score 0.99
Q5Z8S0 · AlphaFold monomer V2.0 prediction for abscisic acid receptor PYL9 (Q5Z8S0) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q5Z8S0
Every structure of UniProt Q0JLP9
Elsewhere: RCSB PDB 4OIC · PDBe 4OIC · UniProt Q5Z8S0 · UniProt Q0JLP9

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