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Mas complex structure of peptide deformylase from xanthomonas oryzae pv oryzae

Analyse Mas complex structure of peptide deformylase from xanthomonas oryzae pv oryzae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CP0
Type: protein
Length: 170 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase; Met-ala-ser
EC: 3.5.1.88
UniProt: Q5H3Z2
Ligands: CD, NA
Pockets: 1 · best druggability 0.33

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide deformylase (EC 3.5.1.88)	protein	167	27% helix, 32% strand	Q5H3Z2
C	Met-ala-ser	protein	3	0% helix, 33% strand	—

Ligands and binding sites

CD · Cadmium ion · metal · 5 copies · chains A, C
NA · Sodium ion · metal · chains A
ACT · Acetate ion · additive · 3 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	89	0.33	0.74	23	CD

Interfaces

1 interface between chains.

A–C · 330 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5CP0 · MAS complex structure of peptide deformylase from Xanthomonas oryzae pv oryzae · 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 Q5H3Z2
Elsewhere: RCSB PDB 5CP0 · PDBe 5CP0 · UniProt Q5H3Z2

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