MolNFT v1 · #71667 · protein + DNA

Structure of SOPB(155-272)-18MER complex, P21 form

3MKZ · Protein sopb: “Structure of SOPB(155-272)-18MER complex, P21 form”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.38). MolNFT v1 #71667 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3MKZ
Type: protein + DNA
Length: 516 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein sopb; DNA (5'- D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
UniProt: P62558
Ligands: CA
Pockets: 8 · best druggability 0.38

Structure

x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein sopb	protein	112	70% helix, 0% strand	P62558
B, U	Protein sopb	protein	111	72% helix, 0% strand	P62558
C, D, Y, Z	DNA (5'- D(CPTPGPGPGPAPCPCPAPTPGPGPTPCPCPCPAPG)-3')	dna	18	—	—
N	Protein sopb	protein	110	69% helix, 0% strand	P62558

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, Z, Y

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	96	0.38	0.76	14	empty
2	78	0.36	0.77	15	empty
3	133	0.36	0.72	24	empty
4	83	0.35	0.75	21	empty
5	90	0.35	0.75	17	empty

Interfaces

9 interfaces between chains.

Y–Z · 799 Å² buried · 80 hydrogen bonds · nucleic-nucleic
C–D · 796 Å² buried · 75 hydrogen bonds · nucleic-nucleic
A–B · 551 Å² buried · 12 hydrogen bonds · protein-protein
D–N · 459 Å² buried · 13 hydrogen bonds · protein-nucleic
U–Y · 445 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

3MKZ · Structure of SopB(155-272)-18mer complex, P21 form · the same entry in another collection · chain N against N, TM-score 1.00
P62558 · AlphaFold monomer V2.0 prediction for protein sopb (P62558) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P62558
Elsewhere: RCSB PDB 3MKZ · PDBe 3MKZ · UniProt P62558

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