MolNFT v1 · #138350 · protein
Estrogen receptor alpha ligand binding domain in complex with estradiol and SRC2-LP1
5WGD: “Estrogen receptor alpha ligand binding domain in complex with estradiol and SRC2-LP1”. X-ray diffraction, 3 ligands (ACE, EST, NH2), 6 pockets (best druggability 0.84). MolNFT v1 #138350 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5WGD
- Type
- protein
- Length
- 471 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; (ACE)HKILHKLLQDS(NH2); (ACE)AILHKLLQDS(NH2)
- UniProt
- P03372
- Ligands
- ACE, EST, NH2
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 228 | 68% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 222 | 72% helix, 4% strand | P03372 |
| E | (ACE)HKILHKLLQDS(NH2) | protein | 11 | 45% helix, 0% strand | — |
| F | (ACE)AILHKLLQDS(NH2) | protein | 10 | 80% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains E, F
- EST · Estradiol · ligand · 2 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.84 | 0.98 | 21 | EST |
| 2 | 182 | 0.84 | 0.98 | 22 | EST |
| 3 | 98 | 0.64 | 0.89 | 18 | empty |
| 4 | 93 | 0.62 | 0.88 | 19 | empty |
| 5 | 254 | 0.58 | 0.78 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1635 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 557 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 491 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 isopeptide (covalent ligand, isopeptide).
Compared structures
- 5WGD · Estrogen Receptor Alpha Ligand Binding Domain in Complex with Estradiol and SRC2-LP1 · the same entry in another collection · chain A against A, TM-score 1.00
- P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P03372
- Elsewhere: RCSB PDB 5WGD · PDBe 5WGD · UniProt P03372
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