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The crystal structure of the N-terminal pas domain of the F plasmid traj

Analyse The crystal structure of the N-terminal pas domain of the F plasmid traj in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KQD
Type: protein
Length: 454 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein traj
UniProt: P06626
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein traj	protein	114	30% helix, 39% strand	P06626
B	Protein traj	protein	116	37% helix, 40% strand	P06626
C	Protein traj	protein	109	28% helix, 37% strand	P06626
D	Protein traj	protein	115	37% helix, 37% strand	P06626

Ligands and binding sites

DTD · Dithiane diol · additive · 2 copies · chains A, B, C, D
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
GOL · Glycerol · additive · chains 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.75	0.99	24	DTD
2	64	0.74	0.98	24	DTD
3	82	0.43	0.80	24	empty
4	126	0.37	0.73	22	empty

Interfaces

3 interfaces between chains.

A–B · 1649 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 1171 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 51 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4KQD · The crystal Structure of the N-terminal PAS domain of the F plasmid TraJ · the same entry in another collection · chain D against D, TM-score 1.00
P06626 · AlphaFold monomer V2.0 prediction for protein traj (P06626) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P06626
Elsewhere: RCSB PDB 4KQD · PDBe 4KQD · UniProt P06626

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