Research workbench
Heme exporter in complex with mn-containing protoporphyrin IX, mn- anomalous data
Analyse Heme exporter in complex with mn-containing protoporphyrin IX, mn- anomalous… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W7A
- Type
- protein
- Length
- 3,370 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ABC transport system, ATP-binding protein; Putative ABC transport system…
- UniProt
- Q6NEF2, Q6NEF1
- Ligands
- MNR, AGA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ABC transport system, ATP-binding protein | protein | 216 | 36% helix, 25% strand | Q6NEF2 |
| B | Putative ABC transport system integral membrane protein | protein | 341 | 54% helix, 19% strand | Q6NEF1 |
| C | Putative ABC transport system, ATP-binding protein | protein | 217 | 35% helix, 26% strand | Q6NEF2 |
| D, F, H | Putative ABC transport system integral membrane protein | protein | 342 | 53% helix, 19% strand | Q6NEF1 |
| E | Putative ABC transport system, ATP-binding protein | protein | 213 | 37% helix, 26% strand | Q6NEF2 |
| G | Putative ABC transport system, ATP-binding protein | protein | 227 | 32% helix, 26% strand | Q6NEF2 |
| I, K | Putative ABC transport system, ATP-binding protein | protein | 222 | 34% helix, 27% strand | Q6NEF2 |
| J, L | Putative ABC transport system integral membrane protein | protein | 343 | 52% helix, 19% strand | Q6NEF1 |
Ligands and binding sites
- MNR · Protoporphyrin IX containing Mn · ligand · 2 copies · chains B, D, F, H
- AGA · (1S)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(pentanoyloxy)methyl]ethyl octanoate · ligand · chains B
- PGE · Triethylene glycol · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains D
- EDO · 1,2-ethanediol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.83 | 0.84 | 106 | MNR |
| 2 | 1094 | 0.79 | 0.81 | 118 | MNR |
| 3 | 1004 | 0.79 | 0.81 | 76 | empty |
| 4 | 1178 | 0.77 | 0.80 | 96 | empty |
| 5 | 1116 | 0.76 | 0.79 | 85 | empty |
Interfaces
18 interfaces between chains.
- F–H · 2192 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 2124 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1207 Ų buried · 12 hydrogen bonds · protein-protein
- J–L · 1166 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1152 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7W7A · Heme exporter in complex with Mn-containing protoporphyrin IX, Mn-anomalous data · 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 Q6NEF2
- Every structure of UniProt Q6NEF1
- Elsewhere: RCSB PDB 7W7A · PDBe 7W7A · UniProt Q6NEF2 · UniProt Q6NEF1
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