MolNFT v1 · #89782 · protein

Crystal structure of amidohydrolase MAP2389C (target efi-500390) from mycobacterium avium subsp. paratuberculosis K-10

4DZI · Putative tim-barrel metal-dependent hydrolase: “Crystal structure of amidohydrolase MAP2389C (target efi-500390) from mycobacterium avium subsp.…”. X-ray diffraction, 4 ligands (CD, MG, CL), 19 pockets (best druggability 0.79).…

PDB: 4DZI
Type: protein
Length: 1,536 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative tim-barrel metal-dependent hydrolase
UniProt: F7P4T2
Ligands: CD, MG, CL, SO4
Pockets: 19 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative tim-barrel metal-dependent hydrolase	protein	384	44% helix, 13% strand	F7P4T2
B, D	Putative tim-barrel metal-dependent hydrolase	protein	382	44% helix, 13% strand	F7P4T2
C	Putative tim-barrel metal-dependent hydrolase	protein	388	44% helix, 13% strand	F7P4T2

Ligands and binding sites

CD · Cadmium ion · metal · 8 copies · chains A, B, C, D
MG · Magnesium ion · metal · chains A
CL · Chloride ion · ion · 6 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 2 copies · chains A, C, B, D

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

Pockets

19 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	832	0.79	0.82	72	CL
2	843	0.78	0.81	73	empty
3	976	0.78	0.80	76	empty
4	1091	0.77	0.79	89	empty
5	93	0.42	0.78	17	empty

Interfaces

6 interfaces between chains.

A–C · 2323 Å² buried · 33 hydrogen bonds · protein-protein
B–D · 2267 Å² buried · 35 hydrogen bonds · protein-protein
A–D · 537 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 537 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 87 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4DZI · Crystal structure of amidohydrolase map2389c (target EFI-500390) from Mycobacterium avium… · 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 F7P4T2
Elsewhere: RCSB PDB 4DZI · PDBe 4DZI · UniProt F7P4T2

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