MolNFT v1 · #46733 · protein

The crystal structure of gene product ATU2144 from agrobacterium tumefaciens

2ODF · Hypothetical protein ATU2144: “The crystal structure of gene product ATU2144 from agrobacterium tumefaciens”. X-ray diffraction, 1 ligand (SO4), 19 pockets (best druggability 0.74). MolNFT v1 #46733 on GenesisL1: 3D structure…

PDB: 2ODF
Type: protein
Length: 2,006 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein ATU2144
UniProt: Q8UDI1
Ligands: SO4
Pockets: 19 · best druggability 0.74

Structure

x-ray diffraction · 5 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein ATU2144	protein	252	39% helix, 17% strand	Q8UDI1
B	Hypothetical protein ATU2144	protein	252	40% helix, 16% strand	Q8UDI1
C	Hypothetical protein ATU2144	protein	249	38% helix, 18% strand	Q8UDI1
D, G	Hypothetical protein ATU2144	protein	250	39% helix, 18% strand	Q8UDI1
E, F, H	Hypothetical protein ATU2144	protein	251	37% helix, 18% strand	Q8UDI1

Ligands and binding sites

SO4 · Sulfate ion · ion · 10 copies · chains B, C, D, F, G, H

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

Pockets

19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1184	0.74	0.77	106	SO4
2	680	0.68	0.76	65	empty
3	259	0.67	0.84	29	SO4
4	235	0.66	0.84	32	empty
5	230	0.64	0.83	31	SO4

Interfaces

8 interfaces between chains.

B–F · 1033 Å² buried · 10 hydrogen bonds · protein-protein
E–G · 806 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 805 Å² buried · 10 hydrogen bonds · protein-protein
C–H · 798 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 455 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2ODF · The crystal structure of gene product Atu2144 from Agrobacterium tumefaciens · 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 Q8UDI1
Elsewhere: RCSB PDB 2ODF · PDBe 2ODF · UniProt Q8UDI1

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