MolNFT v1 · #55411 · protein

Structure of dps from microbacterium arborescens in the high iron form

2YJK · Afp: “Structure of dps from microbacterium arborescens in the high iron form”. X-ray diffraction, 2 ligands (OFE, FE), 20 pockets (best druggability 0.62). MolNFT v1 #55411 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2YJK
Type: protein
Length: 1,819 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 0.62

Structure

x-ray diffraction · 5 distinct chains · 77% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Afp	protein	149	79% helix, 3% strand	Q1X6M4
B, D, E, F, H, K, L	Afp	protein	152	75% helix, 3% strand	Q1X6M4
C	Afp	protein	157	74% helix, 3% strand	Q1X6M4
G	Afp	protein	153	76% helix, 3% strand	Q1X6M4
I, J	Afp	protein	148	79% helix, 3% strand	Q1X6M4

Ligands and binding sites

OFE · Iron(II) oxide · ligand · 11 copies · chains A, B, C, I, D, J, E, F, H, G, K, L
FE · Fe (III) ion · metal · 6 copies · chains B, D, L, A, C, E, G, I, K, H, F, J

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	88	0.62	0.89	16	FE
2	100	0.59	0.86	16	FE
3	356	0.59	0.77	48	empty
4	127	0.59	0.84	23	FE
5	293	0.57	0.77	36	empty

Interfaces

30 interfaces between chains.

G–H · 1426 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1390 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 1381 Å² buried · 22 hydrogen bonds · protein-protein
D–J · 1360 Å² buried · 23 hydrogen bonds · protein-protein
C–I · 1358 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

2YJK · Structure of Dps from MICROBACTERIUM ARBORESCENS in the high 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 2YJK · PDBe 2YJK · UniProt Q1X6M4

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