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Crystal structure of a section of a de novo design gigadalton protein fibre

Analyse Crystal structure of a section of a de novo design gigadalton protein fibre in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RA3
Type: protein
Length: 106 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: P1C; P2F
Ligands: NA
Pockets: 1 · best druggability 0.34

Structure

x-ray diffraction · 4 distinct chains · 84% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	P1C	protein	28	86% helix, 0% strand	—
B	P2F	protein	25	92% helix, 0% strand	—
D	P2F	protein	27	89% helix, 0% strand	—
E	P1C	protein	26	69% helix, 0% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains D, E

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	74	0.34	0.75	18	empty

Interfaces

3 interfaces between chains.

D–E · 729 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 721 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 495 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

3RA3 · Crystal structure of a section of a de novo design gigaDalton protein fibre · 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
Elsewhere: RCSB PDB 3RA3 · PDBe 3RA3

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