Research workbench
Crystal complex of cyclooxygenase-2 with indomethacin-butyldiamine- dansyl conjugate
Analyse Crystal complex of cyclooxygenase-2 with indomethacin-butyldiamine- dansyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BL3
- Type
- protein
- Length
- 2,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin G/H synthase 2
- EC
- 1.14.99.1
- UniProt
- Q05769
- Ligands
- HEM, L7M, NAG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Prostaglandin G/H synthase 2 (EC 1.14.99.1) | protein | 552 | 47% helix, 9% strand | Q05769 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- L7M · 2-[1-(4-chlorobenzene-1-carbonyl)-5-methoxy-2-methyl-1H-indol-3-yl]-N-[4-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)butyl]acetamide · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- BOG · octyl beta-D-glucopyranoside · additive · 6 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.82 | 0.84 | 80 | L7M |
| 2 | 1090 | 0.80 | 0.81 | 95 | L7M |
| 3 | 906 | 0.80 | 0.82 | 75 | L7M |
| 4 | 1082 | 0.80 | 0.81 | 97 | L7M |
| 5 | 687 | 0.79 | 0.84 | 76 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2622 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2618 Ų buried · 50 hydrogen bonds · protein-protein
- A–D · 380 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6BL3 · Crystal Complex of Cyclooxygenase-2 with indomethacin-butyldiamine-dansyl conjugate · 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 Q05769
- Elsewhere: RCSB PDB 6BL3 · PDBe 6BL3 · UniProt Q05769
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