MolNFT v1 · #62992 · protein

Crystal structure of rhizavidin

3EW1: “Crystal structure of rhizavidin”. X-ray diffraction, 13 pockets (best druggability 0.79). MolNFT v1 #62992 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3EW1
Type: protein
Length: 802 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhizavidin
UniProt: Q8KKW2
Pockets: 13 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 63% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Rhizavidin	protein	134	2% helix, 62% strand	Q8KKW2
B, C, D	Rhizavidin	protein	135	7% helix, 62% strand	Q8KKW2
E	Rhizavidin	protein	129	3% helix, 66% strand	Q8KKW2

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1072	0.79	0.81	135	empty
2	447	0.69	0.81	58	empty
3	79	0.56	0.86	18	empty
4	96	0.53	0.83	17	empty
5	93	0.51	0.82	18	empty

Interfaces

12 interfaces between chains.

A–C · 1615 Å² buried · 29 hydrogen bonds · protein-protein
B–E · 1552 Å² buried · 33 hydrogen bonds · protein-protein
D–F · 1518 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 1417 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1391 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3EW1 · Crystal structure of rhizavidin · 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 Q8KKW2
Elsewhere: RCSB PDB 3EW1 · PDBe 3EW1 · UniProt Q8KKW2

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