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PILT4 from geobacter metallireducens bound to ADP with partial occupancy: C3OCOCOC conformation

Analyse PILT4 from geobacter metallireducens bound to ADP with partial occupancy… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OJZ
Type: protein
Length: 2,127 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Twitching motility pilus retraction ATPase
UniProt: Q39VU6
Ligands: ADP
Pockets: 15 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Twitching motility pilus retraction ATPase	protein	355	41% helix, 26% strand	Q39VU6
B, E, F	Twitching motility pilus retraction ATPase	protein	353	40% helix, 26% strand	Q39VU6
C	Twitching motility pilus retraction ATPase	protein	352	40% helix, 26% strand	Q39VU6
D	Twitching motility pilus retraction ATPase	protein	361	41% helix, 25% strand	Q39VU6

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1006	0.85	0.86	120	ADP
2	1190	0.82	0.83	107	ADP
3	934	0.81	0.83	75	ADP
4	1084	0.81	0.82	108	empty
5	944	0.81	0.83	73	ADP

Interfaces

6 interfaces between chains.

E–F · 1691 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 1659 Å² buried · 43 hydrogen bonds · protein-protein
D–E · 1611 Å² buried · 38 hydrogen bonds · protein-protein
C–D · 1579 Å² buried · 36 hydrogen bonds · protein-protein
A–F · 1512 Å² buried · 41 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6OJZ · PilT4 from Geobacter metallireducens bound to ADP with partial occupancy: C3ocococ… · 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 Q39VU6
Elsewhere: RCSB PDB 6OJZ · PDBe 6OJZ · UniProt Q39VU6

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