MolNFT v1 · #165659 · protein

Pmtcd peptide exporter basket domain

6U2D · ABC transporter ATP-binding protein: “Pmtcd peptide exporter basket domain”. X-ray diffraction, 2 ligands (IOD, SO4), 2 pockets (best druggability 0.57). MolNFT v1 #165659 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6U2D
Type: protein
Length: 257 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC transporter ATP-binding protein
UniProt: X5EJW5
Ligands: IOD, SO4
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ABC transporter ATP-binding protein	protein	66	35% helix, 26% strand	X5EJW5
B, D	ABC transporter ATP-binding protein	protein	64	41% helix, 30% strand	X5EJW5
C	ABC transporter ATP-binding protein	protein	63	37% helix, 30% strand	X5EJW5

Ligands and binding sites

IOD · Iodide ion · ion · 7 copies · chains A, B, C
SO4 · Sulfate ion · ion · 5 copies · chains A, D, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	265	0.57	0.78	28	empty
2	50	0.30	0.76	15	IOD

Interfaces

4 interfaces between chains.

A–B · 714 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 362 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 280 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 18 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6U2D · PmtCD peptide exporter basket domain · 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 X5EJW5
Elsewhere: RCSB PDB 6U2D · PDBe 6U2D · UniProt X5EJW5

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