MolNFT v1 · #179806 · protein

S. typhi ycbb - ertapenem complex

7KGN · L,D-transpeptidase: “S. typhi ycbb - ertapenem complex”. X-ray diffraction, 1 ligand (1RG), 9 pockets (best druggability 0.68). MolNFT v1 #179806 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KGN
Type: protein
Length: 462 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L,D-transpeptidase
UniProt: A0A0W3KZB5
Ligands: 1RG
Pockets: 9 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L,D-transpeptidase	protein	462	32% helix, 10% strand	A0A0W3KZB5

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

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	272	0.68	0.83	30	empty
2	79	0.64	0.91	17	empty
3	298	0.58	0.77	39	empty
4	73	0.56	0.87	19	empty
5	124	0.55	0.82	27	empty

Modifications

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

Compared structures

7KGN · S. Typhi 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 A0A0W3KZB5
Elsewhere: RCSB PDB 7KGN · PDBe 7KGN · UniProt A0A0W3KZB5

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