MolNFT v1 · #61053 · protein

A conformationally strained, circular permutant of barnase

3DA7 · Barnase circular permutant: “A conformationally strained, circular permutant of barnase”. X-ray diffraction, 6 pockets (best druggability 0.69). MolNFT v1 #61053 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3DA7
Type: protein
Length: 774 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Barnase circular permutant; Barstar
UniProt: P11540
Pockets: 6 · best druggability 0.69

Structure

x-ray diffraction · 6 distinct chains · 28% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Barnase circular permutant	protein	109	20% helix, 25% strand	—
B	Barnase circular permutant	protein	101	17% helix, 25% strand	—
C, D, F	Barstar	protein	90	47% helix, 19% strand	P11540
E	Barnase circular permutant	protein	103	20% helix, 24% strand	—
G	Barnase circular permutant	protein	102	17% helix, 25% strand	—
H	Barstar	protein	89	51% helix, 18% strand	P11540

Pockets

6 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	534	0.69	0.79	45	empty
2	136	0.44	0.76	26	empty
3	120	0.42	0.76	20	empty
4	112	0.42	0.77	24	empty
5	106	0.42	0.77	26	empty

Interfaces

7 interfaces between chains.

G–H · 842 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 834 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 823 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 809 Å² buried · 18 hydrogen bonds · protein-protein
D–H · 581 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3DA7 · A conformationally strained, circular permutant of barnase · the same entry in another collection · chain H against H, TM-score 1.00
P11540 · AlphaFold monomer V2.0 prediction for barstar (P11540) · a predicted model of the same protein · chain C 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 P11540
Elsewhere: RCSB PDB 3DA7 · PDBe 3DA7 · UniProt P11540

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