MolNFT v1 · #129288 · protein

Structure of the antibacterial peptide ABC transporter mcjd in a high energy outward occluded intermediate state

5OFR · Microcin-J25 export ATP-BINDING/PERMEASE protein mcjd: “Structure of the antibacterial peptide ABC transporter mcjd in a high energy outward occluded intermediate…”. X-ray diffraction, 3 ligands (ADP, MG, VO4), 19 pockets (best…

PDB: 5OFR
Type: protein
Length: 1,147 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Microcin-J25 export ATP-BINDING/PERMEASE protein mcjd
UniProt: Q9X2W0
Ligands: ADP, MG, VO4
Pockets: 19 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 63% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Microcin-J25 export ATP-BINDING/PERMEASE protein mcjd	protein	571	63% helix, 11% strand	Q9X2W0
B	Microcin-J25 export ATP-BINDING/PERMEASE protein mcjd	protein	576	64% helix, 10% strand	Q9X2W0

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
VO4 · Vanadate ion · ion · 2 copies · chains A, B

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

Pockets

19 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	396	0.81	0.89	43	empty
2	513	0.80	0.87	57	empty
3	287	0.80	0.92	28	empty
4	498	0.80	0.86	61	empty
5	534	0.78	0.85	63	ADP, MG, VO4

Interfaces

1 interface between chains.

A–B · 7480 Å² buried · 77 hydrogen bonds · protein-protein

Compared structures

5OFR · Structure of the antibacterial peptide ABC transporter McjD in a high energy outward… · the same entry in another collection · chain A against A, TM-score 1.00
Q9X2W0 · AlphaFold monomer V2.0 prediction for microcin-J25 export ATP- BINDING/PERMEASE protein… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9X2W0
Elsewhere: RCSB PDB 5OFR · PDBe 5OFR · UniProt Q9X2W0

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