MolNFT v1 · #179805 · protein

C. rodentium ycbb - ertapenem complex

7KGM · Putative exported protein: “C. rodentium ycbb - ertapenem complex”. X-ray diffraction, 1 ligand (1RG), 4 pockets (best druggability 0.61). MolNFT v1 #179805 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KGM
Type: protein
Length: 512 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative exported protein
UniProt: D2TS62
Ligands: 1RG
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative exported protein	protein	512	42% helix, 13% strand	D2TS62

Ligands and binding sites

1RG · (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl) carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	187	0.61	0.82	21	empty
2	356	0.59	0.77	43	empty
3	182	0.49	0.76	30	1RG
4	134	0.48	0.78	17	empty

Modifications

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

Compared structures

7KGM · C. rodentium YcbB - ertapenem complex · 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 D2TS62
Elsewhere: RCSB PDB 7KGM · PDBe 7KGM · UniProt D2TS62

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