MolNFT v1 · #88713 · protein

Structure of psta

4D3H: “Structure of psta”. X-ray diffraction, 1 ligand (2BA), 4 pockets (best druggability 0.72). MolNFT v1 #88713 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4D3H
Type: protein
Length: 308 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Psta
UniProt: Q99WC0
Ligands: 2BA
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Psta	protein	103	27% helix, 46% strand	Q99WC0
B	Psta	protein	104	27% helix, 45% strand	Q99WC0
C	Psta	protein	101	28% helix, 41% strand	Q99WC0

Ligands and binding sites

2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · 3 copies · chains A, B, C

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.72	0.97	17	empty
2	336	0.65	0.80	43	2BA
3	342	0.62	0.78	41	2BA
4	259	0.57	0.77	38	2BA

Interfaces

3 interfaces between chains.

A–B · 998 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 985 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 940 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4D3H · Structure of PstA · 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 Q99WC0
Elsewhere: RCSB PDB 4D3H · PDBe 4D3H · UniProt Q99WC0

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