MolNFT v1 · #148670 · protein

Crystal structure of the HHD2 domain of whirlin

6FDD: “Crystal structure of the HHD2 domain of whirlin”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.60). MolNFT v1 #148670 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6FDD
Type: protein
Length: 456 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Whirlin
UniProt: Q80VW5
Ligands: SO4
Pockets: 4 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E	Whirlin	protein	76	74% helix, 0% strand	Q80VW5
C	Whirlin	protein	77	74% helix, 0% strand	Q80VW5
F	Whirlin	protein	75	69% helix, 0% strand	Q80VW5

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains B, E, D, F, 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	395	0.60	0.76	33	empty
2	391	0.59	0.76	33	empty
3	364	0.58	0.76	38	empty
4	50	0.27	0.75	14	empty

Interfaces

9 interfaces between chains.

C–F · 585 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 566 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 561 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 561 Å² buried · 7 hydrogen bonds · protein-protein
A–F · 554 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

6FDD · Crystal Structure of the HHD2 Domain of Whirlin · the same entry in another collection · chain F against F, TM-score 1.00
Q80VW5 · AlphaFold monomer V2.0 prediction for whirlin (Q80VW5) · a predicted model of the same protein · chain F against A, TM-score 0.93

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 Q80VW5
Elsewhere: RCSB PDB 6FDD · PDBe 6FDD · UniProt Q80VW5

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