MolNFT v1 · #122432 · protein

Pha binding protein phap (phasin)

5IP0 · Pha granule-associated protein: “Pha binding protein phap (phasin)”. X-ray diffraction, 1 ligand (CD), 18 pockets (best druggability 0.83). MolNFT v1 #122432 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IP0
Type: protein
Length: 1,572 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pha granule-associated protein
UniProt: O32470
Ligands: CD
Pockets: 18 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 93% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I, M	Pha granule-associated protein	protein	107	93% helix, 0% strand	O32470
B, F, J, N	Pha granule-associated protein	protein	88	95% helix, 0% strand	O32470
C, G, K, O	Pha granule-associated protein	protein	90	94% helix, 0% strand	O32470
D, H, L, P	Pha granule-associated protein	protein	108	92% helix, 0% strand	O32470

Ligands and binding sites

CD · Cadmium ion · metal · 29 copies · chains A, B, L, C, D, H, G, E, F, I, J, M, N, K, P

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

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1162	0.83	0.84	118	CD
2	300	0.81	0.92	30	CD
3	456	0.81	0.89	32	CD
4	530	0.70	0.79	55	CD
5	471	0.70	0.80	65	CD

Interfaces

39 interfaces between chains.

I–K · 1860 Å² buried · 13 hydrogen bonds · protein-protein
E–G · 1809 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 1806 Å² buried · 11 hydrogen bonds · protein-protein
M–O · 1804 Å² buried · 10 hydrogen bonds · protein-protein
J–L · 1568 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5IP0 · PHA Binding Protein PhaP (Phasin) · 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 O32470
Elsewhere: RCSB PDB 5IP0 · PDBe 5IP0 · UniProt O32470

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