MolNFT v1 · #55410 · protein

Structure of dps from microbacterium arborescens in the low iron form

2YJJ · Afp: “Structure of dps from microbacterium arborescens in the low iron form”. X-ray diffraction, 2 ligands (OFE, FE), 20 pockets (best druggability 0.60). MolNFT v1 #55410 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2YJJ
Type: protein
Length: 1,796 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Afp
UniProt: Q1X6M4
Ligands: OFE, FE
Pockets: 20 · best druggability 0.60

Structure

x-ray diffraction · 6 distinct chains · 78% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, K	Afp	protein	149	79% helix, 3% strand	Q1X6M4
B	Afp	protein	151	77% helix, 3% strand	Q1X6M4
D, I, J	Afp	protein	148	78% helix, 3% strand	Q1X6M4
E, F, L	Afp	protein	150	78% helix, 3% strand	Q1X6M4
G	Afp	protein	157	75% helix, 3% strand	Q1X6M4
H	Afp	protein	147	79% helix, 3% strand	Q1X6M4

Ligands and binding sites

OFE · Iron(II) oxide · ligand · 10 copies · chains A, B, C, E, I, D, J, F, G, H, K, L
FE · Fe (III) ion · metal · 2 copies · chains A, B, K, L

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	100	0.60	0.87	17	empty
2	288	0.59	0.78	42	empty
3	346	0.58	0.76	51	empty
4	94	0.58	0.87	16	empty
5	104	0.58	0.86	17	empty

Interfaces

30 interfaces between chains.

G–H · 1390 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1385 Å² buried · 23 hydrogen bonds · protein-protein
C–I · 1372 Å² buried · 24 hydrogen bonds · protein-protein
K–L · 1360 Å² buried · 22 hydrogen bonds · protein-protein
D–J · 1358 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

2YJJ · Structure of Dps from MICROBACTERIUM ARBORESCENS in the low iron form · 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 Q1X6M4
Elsewhere: RCSB PDB 2YJJ · PDBe 2YJJ · UniProt Q1X6M4

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