MolNFT v1 · #180770 · protein
Crystal structure of myeloperoxidase subform C (mpo) complex with compound-30 aka 7-[(3~{S},4~{R},6~{R})-4-benzyl-2-oxa-7,13,14- TRIAZATETRACYCLO[14.3.1.1^{3,6}.1^{11,14}]DOCOSA-1(19),11(21),12, 16(20),17-pentaen-10-yl]-3~{H}-TRIAZOLO[4,5-B]PYRIDIN-5-amine
7LAN · Myeloperoxidase light chain: “Crystal structure of myeloperoxidase subform C (mpo) complex with compound-30 aka…”. X-ray diffraction, 8 ligands (HEM, XS1, NAG), 20 pockets (best druggability 0.81). MolNFT v1 #180770 on GenesisL1: 3D…
- PDB
- 7LAN
- Type
- protein
- Length
- 2,270 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase light chain; Isoform H14 of myeloperoxidase
- EC
- 1.11.2.2
- UniProt
- P05164
- Ligands
- HEM, XS1, NAG, MAN, BMA, FUC, CA, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, H | Myeloperoxidase light chain (EC 1.11.2.2) | protein | 103 | 25% helix, 11% strand | P05164 |
| B, G, I | Isoform H14 of myeloperoxidase (EC 1.11.2.2) | protein | 464 | 41% helix, 8% strand | P05164 |
| D | Myeloperoxidase light chain (EC 1.11.2.2) | protein | 104 | 25% helix, 11% strand | P05164 |
| E | Isoform H14 of myeloperoxidase (EC 1.11.2.2) | protein | 465 | 40% helix, 8% strand | P05164 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, D, E, F, G, H, I
- XS1 · 7-[(3R,4S,6S,10R)-4-benzyl-2-oxa-7,13,14-triazatetracyclo[14.3.1.1~3,6~.1~11,14~]docosa-1(20), 11(21),12,16,18-pentaen-10-yl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine · ligand · 4 copies · chains A, B, D, E, F, G, H, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains B, E, D, A, G, I, H, F
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains E, D, B, A, I, H, G, F
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains E, B, I, G
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, E, G, I
- CA · Calcium ion · metal · 4 copies · chains A, B, D, E, F, G, H, I
- CL · Chloride ion · ion · 4 copies · chains A, B, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.81 | 0.85 | 65 | empty |
| 2 | 986 | 0.80 | 0.82 | 77 | HEM, XS1 |
| 3 | 697 | 0.79 | 0.84 | 60 | MAN |
| 4 | 768 | 0.78 | 0.82 | 55 | HEM, XS1 |
| 5 | 687 | 0.78 | 0.82 | 52 | HEM, XS1 |
Interfaces
14 interfaces between chains.
- A–B · 5754 Ų buried · 110 hydrogen bonds · protein-protein
- F–G · 5743 Ų buried · 108 hydrogen bonds · protein-protein
- D–E · 5703 Ų buried · 104 hydrogen bonds · protein-protein
- H–I · 5691 Ų buried · 102 hydrogen bonds · protein-protein
- A–D · 652 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 12 glycan, 9 disulfide (heme attachment, N-glycosylation, disulfide).
Compared structures
- 7LAN · CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH COMPOUND-30 AKA… · 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 P05164
- Elsewhere: RCSB PDB 7LAN · PDBe 7LAN · UniProt P05164
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.