Research workbench
Closed conformation of the Membrane Attack Complex
Analyse Closed conformation of the Membrane Attack Complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H04
- Type
- protein
- Length
- 12,773 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 5.6
- Source
- Homo sapiens
- Molecule
- Complement component C9; Complement C5,Complement C5; Complement component C8 beta chain…
- UniProt
- P02748, P01031, P07358, P10643, P07360, P07357, P13671
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 5.6 · 7 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M, N, O, Q, R, S, T, U, V, W, X, P, H, I, J, K, G | Complement component C9 | protein | 501 | 13% helix, 38% strand | P02748 |
| A | Complement C5,Complement C5 | protein | 1219 | 17% helix, 33% strand | P01031 |
| C | Complement component C8 beta chain | protein | 513 | 12% helix, 43% strand | P07358 |
| D | Complement component C7 | protein | 660 | 13% helix, 29% strand | P10643 |
| E | Complement component C8 gamma chain | protein | 165 | 17% helix, 42% strand | P07360 |
| F | Complement component C8 alpha chain | protein | 510 | 13% helix, 40% strand | P07357 |
| B | Complement component C6 | protein | 688 | 12% helix, 34% strand | P13671 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 76 copies · chains L, M, N, O, Q, R, S, T, U, V, W, X, P, H, I, J, K, G, C, D, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.89 | 0.90 | 142 | empty |
| 2 | 787 | 0.88 | 0.91 | 114 | empty |
| 3 | 988 | 0.88 | 0.90 | 138 | empty |
| 4 | 515 | 0.86 | 0.93 | 89 | empty |
| 5 | 1121 | 0.86 | 0.87 | 146 | empty |
Interfaces
44 interfaces between chains.
- P–G · 4831 Ų buried · 86 hydrogen bonds · protein-protein
- M–N · 4829 Ų buried · 89 hydrogen bonds · protein-protein
- O–Q · 4826 Ų buried · 88 hydrogen bonds · protein-protein
- N–O · 4819 Ų buried · 90 hydrogen bonds · protein-protein
- R–S · 4818 Ų buried · 92 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 264 disulfide, 57 glycan (disulfide, N-glycosylation).
Compared structures
- 6H04 · Closed conformation of the membrane attack complex · the same entry in another collection · chain K against K, 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 P02748
- Every structure of UniProt P01031
- Every structure of UniProt P07358
- Every structure of UniProt P10643
- Every structure of UniProt P07360
- Every structure of UniProt P07357
- Every structure of UniProt P13671
- Elsewhere: RCSB PDB 6H04 · PDBe 6H04 · UniProt P02748 · UniProt P01031 · UniProt P07358 · UniProt P10643 · UniProt P07360 · UniProt P07357 · UniProt P13671
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