MolNFT v1 · #172253 · protein + RNA

Crystal structure of E. COLI RNA helicase hrpa in complex with RNA

6ZWW · ATP-dependent RNA helicase hrpa: “Crystal structure of E. COLI RNA helicase hrpa in complex with RNA”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.89). MolNFT v1 #172253 on GenesisL1: 3D structure, binding…

PDB: 6ZWW
Type: protein + RNA
Length: 3,003 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent RNA helicase hrpa; Ssrna
EC: 3.6.4.13
UniProt: A0A167DLY9
Ligands: CA
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 6 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-dependent RNA helicase hrpa (EC 3.6.4.13)	protein	744	42% helix, 19% strand	A0A167DLY9
C	ATP-dependent RNA helicase hrpa (EC 3.6.4.13)	protein	749	43% helix, 18% strand	A0A167DLY9
E	ATP-dependent RNA helicase hrpa (EC 3.6.4.13)	protein	731	43% helix, 19% strand	A0A167DLY9
G	ATP-dependent RNA helicase hrpa (EC 3.6.4.13)	protein	735	44% helix, 19% strand	A0A167DLY9
B, D	Ssrna	rna	12	—	—
F, H	Ssrna	rna	10	—	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, C, E, G

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	1084	0.89	0.91	126	empty
2	1033	0.89	0.90	128	empty
3	1122	0.89	0.90	127	empty
4	225	0.79	0.93	40	empty
5	740	0.79	0.83	73	empty

Interfaces

7 interfaces between chains.

E–G · 2192 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 2181 Å² buried · 35 hydrogen bonds · protein-protein
E–F · 1607 Å² buried · 37 hydrogen bonds · protein-nucleic
C–D · 1604 Å² buried · 35 hydrogen bonds · protein-nucleic
A–B · 1602 Å² buried · 23 hydrogen bonds · protein-nucleic

Compared structures

6ZWW · Crystal structure of E. coli RNA helicase HrpA in complex with RNA · 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 A0A167DLY9
Elsewhere: RCSB PDB 6ZWW · PDBe 6ZWW · UniProt A0A167DLY9

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