MolNFT v1 · #146204 · protein

Phdj wt 2 ångströms resolution

6DAN: “Phdj wt 2 ångströms resolution”. X-ray diffraction, 1 ligand (CL), 8 pockets (best druggability 0.77). MolNFT v1 #146204 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DAN
Type: protein
Length: 1,302 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phdj
UniProt: Q6H2K0
Ligands: CL
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phdj	protein	323	51% helix, 11% strand	Q6H2K0
B	Phdj	protein	328	50% helix, 11% strand	Q6H2K0
C	Phdj	protein	328	50% helix, 11% strand	Q6H2K0
D	Phdj	protein	323	51% helix, 12% strand	Q6H2K0

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	571	0.77	0.84	63	empty
2	563	0.77	0.83	58	empty
3	524	0.77	0.84	62	empty
4	567	0.77	0.83	66	empty
5	199	0.59	0.81	26	empty

Interfaces

4 interfaces between chains.

B–D · 2058 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 2016 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 703 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 687 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6DAN · PhdJ WT 2 Angstroms resolution · 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 Q6H2K0
Elsewhere: RCSB PDB 6DAN · PDBe 6DAN · UniProt Q6H2K0

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