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Crystal structure of rhodospirillum rubrum RRU_A0973 mutant E32A, E62A, H65A.

Analyse Crystal structure of rhodospirillum rubrum RRU_A0973 mutant E32A, E62A, H65A. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5L8F
Type: protein
Length: 898 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RRU_A0973
UniProt: Q2RVS1
Ligands: MG
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, F	RRU_A0973	protein	89	79% helix, 0% strand	Q2RVS1
B, G, I	RRU_A0973	protein	91	79% helix, 0% strand	Q2RVS1
D	RRU_A0973	protein	88	78% helix, 0% strand	Q2RVS1
E, H, J	RRU_A0973	protein	90	78% helix, 0% strand	Q2RVS1

Ligands and binding sites

MG · Magnesium ion · metal · 10 copies · chains B, C, D, E, F, H, G, I, J
PGE · Triethylene glycol · additive · chains G, I

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	148	0.77	0.94	27	empty
2	131	0.74	0.93	22	empty
3	205	0.72	0.88	36	PGE
4	296	0.70	0.84	53	empty
5	210	0.69	0.86	35	empty

Interfaces

20 interfaces between chains.

G–H · 2581 Å² buried · 42 hydrogen bonds · protein-protein
I–J · 2580 Å² buried · 52 hydrogen bonds · protein-protein
A–B · 2572 Å² buried · 48 hydrogen bonds · protein-protein
C–D · 2538 Å² buried · 44 hydrogen bonds · protein-protein
E–F · 2530 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

5L8F · Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant E32A, E62A, H65A. · 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 Q2RVS1
Elsewhere: RCSB PDB 5L8F · PDBe 5L8F · UniProt Q2RVS1

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