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Phdj bound to substrate intermediate

Analyse Phdj bound to substrate intermediate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DAQ
Type: protein
Length: 1,292 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phdj
UniProt: Q6H2K0
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).

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

Pockets

10 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	460	0.74	0.83	59	empty
2	335	0.70	0.83	42	empty
3	356	0.67	0.81	40	empty
4	346	0.66	0.81	42	empty
5	205	0.58	0.80	26	empty

Interfaces

4 interfaces between chains.

A–B · 2000 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 1999 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 656 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 624 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

6DAQ · PhdJ bound to substrate intermediate · 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 6DAQ · PDBe 6DAQ · UniProt Q6H2K0

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