MolNFT v1 · #99852 · protein

Crystal structure of a putative phosphonomutase from burkholderia cenocepacia J2315

4MG4: “Crystal structure of a putative phosphonomutase from burkholderia cenocepacia J2315”. X-ray diffraction, 1 ligand (CL), 18 pockets (best druggability 0.77). MolNFT v1 #99852 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4MG4
Type: protein
Length: 1,998 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphonomutase
UniProt: B4EL08
Ligands: CL
Pockets: 18 · best druggability 0.77

Structure

x-ray diffraction · 7 distinct chains · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphonomutase	protein	250	49% helix, 13% strand	B4EL08
B	Phosphonomutase	protein	251	49% helix, 13% strand	B4EL08
C, E	Phosphonomutase	protein	253	50% helix, 13% strand	B4EL08
D	Phosphonomutase	protein	246	48% helix, 13% strand	B4EL08
F	Phosphonomutase	protein	250	48% helix, 13% strand	B4EL08
G	Phosphonomutase	protein	252	50% helix, 13% strand	B4EL08
H	Phosphonomutase	protein	243	51% helix, 14% strand	B4EL08

Ligands and binding sites

CL · Chloride ion · ion · 25 copies · chains A, B, C, D, E, F, G, H
EDO · 1,2-ethanediol · additive · 4 copies · chains B, D, E, F, H

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

Pockets

18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	119	0.77	0.96	22	empty
2	91	0.70	0.94	21	empty
3	123	0.68	0.90	22	empty
4	121	0.68	0.90	23	empty
5	169	0.59	0.83	33	CL

Interfaces

9 interfaces between chains.

C–E · 1469 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 1393 Å² buried · 11 hydrogen bonds · protein-protein
A–H · 1353 Å² buried · 8 hydrogen bonds · protein-protein
D–G · 1341 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 515 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4MG4 · Crystal structure of a putative phosphonomutase from Burkholderia cenocepacia J2315 · 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 B4EL08
Elsewhere: RCSB PDB 4MG4 · PDBe 4MG4 · UniProt B4EL08

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