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

Analyse Crystal structure of est-Y29, a novel penicillin-binding PROTEIN/BETA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4P87
Type: protein
Length: 777 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Est-Y29
Ligands: 4NP
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Est-Y29	protein	390	31% helix, 17% strand	—
B	Est-Y29	protein	387	30% helix, 19% strand	—

Ligands and binding sites

4NP · 4-nitrophenyl phosphate · ligand · 2 copies · chains A, B

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

Pockets

8 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	898	0.81	0.83	83	4NP
2	876	0.80	0.83	78	4NP
3	65	0.31	0.74	11	empty
4	59	0.30	0.75	16	empty
5	52	0.28	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 1068 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4P87 · 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 4P87 · PDBe 4P87

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