MolNFT v1 · #122085 · protein

Structure of a computationally designed 17-ohp binder

5IER · OHP9: “Structure of a computationally designed 17-ohp binder”. X-ray diffraction, 3 ligands (3QZ, NA, SO4), 7 pockets (best druggability 0.83). MolNFT v1 #122085 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IER
Type: protein
Length: 519 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: OHP9
Ligands: 3QZ, NA, SO4
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	OHP9	protein	131	26% helix, 44% strand	—
D	OHP9	protein	126	28% helix, 40% strand	—

Ligands and binding sites

3QZ · (9beta)-17-hydroxypregn-4-ene-3,20-dione · ligand · 4 copies · chains A, B, C, D
NA · Sodium ion · metal · 4 copies · chains A, D
SO4 · Sulfate ion · ion · 5 copies · chains A, C, B, D

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1116	0.83	0.83	98	3QZ
2	324	0.78	0.88	33	3QZ
3	313	0.77	0.87	33	3QZ
4	116	0.41	0.77	16	empty
5	98	0.36	0.74	19	empty

Interfaces

4 interfaces between chains.

A–D · 978 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 689 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 274 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 225 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5IER · Structure of a computationally designed 17-OHP binder · 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
Elsewhere: RCSB PDB 5IER · PDBe 5IER

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