Research workbench
Crystal structure of anti-MSP2 fv fragment (MAB4D11) in complex with 3D7-MSP2 215-222
Analyse Crystal structure of anti-MSP2 fv fragment (MAB4D11) in complex with 3D7-MSP2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TBD
- Type
- protein
- Length
- 930 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fv fragment (MAB4D1) heavy chain; Merozoite surface protein 2
- Ligands
- ACE, NH2
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, D, J | Fv fragment (MAB4D1) heavy chain | protein | 113 | 11% helix, 52% strand | — |
| F | Fv fragment (MAB4D1) heavy chain | protein | 111 | 3% helix, 49% strand | — |
| I, C, H, L | Merozoite surface protein 2 | protein | 8 | 0% helix, 0% strand | — |
| A | Fv fragment (MAB4D1) heavy chain | protein | 114 | 11% helix, 53% strand | — |
| B | Fv fragment (MAB4D1) heavy chain | protein | 110 | 3% helix, 47% strand | — |
| G, K | Fv fragment (MAB4D1) heavy chain | protein | 112 | 3% helix, 48% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains I, D, H, C, J, L, E, A
- NH2 · Amino group · ion · 4 copies · chains I, A, B, C, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.78 | 0.83 | 93 | ACE |
| 2 | 498 | 0.71 | 0.81 | 51 | NH2 |
| 3 | 116 | 0.49 | 0.80 | 34 | empty |
| 4 | 174 | 0.45 | 0.75 | 39 | empty |
| 5 | 64 | 0.40 | 0.80 | 17 | empty |
Interfaces
29 interfaces between chains.
- E–F · 687 Ų buried · 6 hydrogen bonds · protein-protein
- J–K · 687 Ų buried · 4 hydrogen bonds · protein-protein
- D–G · 684 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 652 Ų buried · 7 hydrogen bonds · protein-protein
- D–J · 383 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 5TBD · Crystal Structure of anti-MSP2 Fv fragment (mAb4D11) in complex with 3D7-MSP2 215-222 · the same entry in another collection · chain E against E, 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
- Elsewhere: RCSB PDB 5TBD · PDBe 5TBD
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