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ABC transporter modbc in complex with its binding protein moda

Analyse ABC transporter modbc in complex with its binding protein moda in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ONK
Type: protein
Length: 2,589 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MOLYBDATE/TUNGSTATE ABC transporter, ATP-binding protein; MOLYBDATE/TUNGSTATE ABC…
UniProt: O30144, O30143, O30142
Ligands: MG, PO4, WO4
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F, G	MOLYBDATE/TUNGSTATE ABC transporter, ATP-binding protein	protein	240	38% helix, 22% strand	O30144
C, D, H, I	MOLYBDATE/TUNGSTATE ABC transporter, permease protein	protein	252	79% helix, 0% strand	O30143
E	MOLYBDATE/TUNGSTATE binding protein	protein	311	33% helix, 25% strand	O30142
J	MOLYBDATE/TUNGSTATE binding protein	protein	310	33% helix, 25% strand	O30142

Ligands and binding sites

MG · Magnesium ion · metal · 6 copies · chains A, B, F, G, E, J
PO4 · Phosphate ion · ion · 4 copies · chains A, B, F, G
WO4 · Tungstate(vi)ion · ion · 2 copies · chains E, J

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1104	0.79	0.81	86	empty
2	1124	0.79	0.80	93	empty
3	431	0.78	0.87	58	empty
4	777	0.78	0.82	86	empty
5	389	0.78	0.87	67	empty

Interfaces

17 interfaces between chains.

H–I · 3739 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 3723 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1484 Å² buried · 1 hydrogen bond · protein-protein
F–G · 1441 Å² buried · 0 hydrogen bonds · protein-protein
F–H · 942 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2ONK · ABC transporter ModBC in complex with its binding protein ModA · the same entry in another collection · chain J against J, TM-score 1.00
O30142 · AlphaFold monomer V2.0 prediction for MOLYBDATE/TUNGSTATE-binding protein wtpa (O30142) · a predicted model of the same protein · chain E 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 O30144
Every structure of UniProt O30143
Every structure of UniProt O30142
Elsewhere: RCSB PDB 2ONK · PDBe 2ONK · UniProt O30144 · UniProt O30143 · UniProt O30142

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