MolNFT v1 · #185555 · protein

Crystal structure of the peptide transporter yepept-K314A in complex with lznv at 2.66 a

7Q0M: “Crystal structure of the peptide transporter yepept-K314A in complex with lznv at 2.66 a”. X-ray diffraction, 2 ligands (OPK, UMQ), 5 pockets (best druggability 0.80). MolNFT v1 #185555 on GenesisL1: 3D structure, binding sites and…

PDB: 7Q0M
Type: protein
Length: 482 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide transporter yepept
UniProt: A0A2R9TD79
Ligands: OPK, UMQ
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 80% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide transporter yepept	protein	482	80% helix, 1% strand	A0A2R9TD79

Ligands and binding sites

OPK · (2~{S})-2-[[(2~{S})-2-azanyl-6-[(4-nitrophenyl) methoxycarbonylamino]hexanoyl]amino]-3-methyl-butanoic acid · ligand · chains A
UMQ · Undecyl-maltoside · ligand · chains A

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	890	0.80	0.82	79	OPK, UMQ
2	590	0.67	0.76	41	empty
3	178	0.52	0.78	26	empty
4	118	0.42	0.76	20	empty
5	58	0.27	0.72	12	empty

Compared structures

7Q0M · Crystal structure of the peptide transporter YePEPT-K314A in complex with LZNV at 2.66 A · 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 A0A2R9TD79
Elsewhere: RCSB PDB 7Q0M · PDBe 7Q0M · UniProt A0A2R9TD79

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