MolNFT v1 · #128946 · protein

X-ray crystal structure of rapz from escherichia COLI (P3221 space group)

5O5Q · RNase adapter protein rapz: “X-ray crystal structure of rapz from escherichia COLI (P3221 space group)”. X-ray diffraction, 1 ligand (SO4), 16 pockets (best druggability 0.76). MolNFT v1 #128946 on GenesisL1: 3D structure, binding…

PDB: 5O5Q
Type: protein
Length: 1,067 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNase adapter protein rapz
UniProt: P0A894
Ligands: SO4
Pockets: 16 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNase adapter protein rapz	protein	265	42% helix, 21% strand	P0A894
B	RNase adapter protein rapz	protein	272	43% helix, 17% strand	P0A894
D	RNase adapter protein rapz	protein	276	42% helix, 20% strand	P0A894
C	RNase adapter protein rapz	protein	254	43% helix, 19% strand	P0A894

Ligands and binding sites

SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D

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

Pockets

16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	976	0.76	0.79	78	SO4
2	218	0.71	0.87	36	empty
3	544	0.68	0.78	60	SO4
4	379	0.66	0.79	31	empty
5	535	0.63	0.75	41	empty

Interfaces

5 interfaces between chains.

A–D · 1505 Å² buried · 23 hydrogen bonds · protein-protein
D–C · 1451 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1437 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 1390 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 138 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5O5Q · X-ray crystal structure of RapZ from Escherichia coli (P3221 space group) · the same entry in another collection · chain C against C, TM-score 1.00
P0A894 · AlphaFold monomer V2.0 prediction for RNase adapter protein rapz (P0A894) · a predicted model of the same protein · chain A against A, TM-score 0.58

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 P0A894
Elsewhere: RCSB PDB 5O5Q · PDBe 5O5Q · UniProt P0A894

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