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Crystal structure of full length RV0805 in complex with 5'-AMP

Analyse Crystal structure of full length RV0805 in complex with 5'-AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IB8
Type: protein
Length: 295 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Icc protein
EC: 3.1.4.17
UniProt: O06629
Ligands: AMP, FE, MN
Pockets: 2 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Icc protein (EC 3.1.4.17)	protein	295	26% helix, 25% strand	O06629

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · chains A
FE · Fe (III) ion · metal · chains A
MN · Manganese (II) ion · metal · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
ACT · Acetate ion · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	149	0.53	0.80	27	AMP
2	89	0.43	0.79	16	MPD

Compared structures

3IB8 · Crystal structure of full length Rv0805 in complex with 5'-AMP · 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 O06629
Elsewhere: RCSB PDB 3IB8 · PDBe 3IB8 · UniProt O06629

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