MolNFT v1 · #103163 · protein

Crystal structure of est-Y29, a novel penicillin-binding PROTEIN/BETA- lactamase homolog from a metagenomic library

4P85: “Crystal structure of est-Y29, a novel penicillin-binding PROTEIN/BETA- lactamase homolog from a metagenomic…”. X-ray diffraction, 1 ligand (DEP), 7 pockets (best druggability 0.78). MolNFT v1 #103163 on GenesisL1: 3D structure…

PDB: 4P85
Type: protein
Length: 777 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Est-Y29
Ligands: DEP
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Est-Y29	protein	390	30% helix, 17% strand	—
B	Est-Y29	protein	387	29% helix, 18% strand	—

Ligands and binding sites

DEP · Diethyl phosphonate · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	641	0.78	0.83	53	DEP
2	602	0.76	0.82	63	DEP
3	180	0.60	0.82	31	empty
4	186	0.58	0.81	38	empty
5	74	0.32	0.74	11	empty

Interfaces

1 interface between chains.

A–B · 1045 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

4P85 · Crystal structure of Est-Y29, a novel penicillin-binding protein/beta-lactamase homolog… · 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
Elsewhere: RCSB PDB 4P85 · PDBe 4P85

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