MolNFT v1 · #141892 · protein

Structure of the type IV phosphorothioation-dependent restriction endonuclease scomcra

5ZMM · Uncharacterized protein mcra: “Structure of the type IV phosphorothioation-dependent restriction endonuclease scomcra”. X-ray diffraction, 2 ligands (ZN, SO4), 20 pockets (best druggability 0.82). MolNFT v1 #141892 on GenesisL1: 3D…

PDB: 5ZMM
Type: protein
Length: 3,029 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein mcra
UniProt: Q9L0M9
Ligands: ZN, SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein mcra	protein	530	40% helix, 18% strand	Q9L0M9
B	Uncharacterized protein mcra	protein	527	42% helix, 17% strand	Q9L0M9
C	Uncharacterized protein mcra	protein	522	43% helix, 15% strand	Q9L0M9
D	Uncharacterized protein mcra	protein	489	40% helix, 16% strand	Q9L0M9
E	Uncharacterized protein mcra	protein	499	42% helix, 16% strand	Q9L0M9
F	Uncharacterized protein mcra	protein	462	41% helix, 17% strand	Q9L0M9

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 11 copies · chains A, C, B, E, D, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	937	0.82	0.83	102	SO4
2	169	0.81	0.96	24	empty
3	1050	0.80	0.81	97	SO4
4	977	0.79	0.81	88	SO4
5	654	0.79	0.84	87	empty

Interfaces

9 interfaces between chains.

A–B · 1928 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1885 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1833 Å² buried · 22 hydrogen bonds · protein-protein
D–F · 559 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 533 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5ZMM · Structure of the Type IV phosphorothioation-dependent restriction endonuclease ScoMcrA · 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 Q9L0M9
Elsewhere: RCSB PDB 5ZMM · PDBe 5ZMM · UniProt Q9L0M9

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