MolNFT v1 · #159887 · protein
HYHEL10 Fab variant HYHEL10-4X (heavy chain mutations L4F, Y33H, S56N, and Y58F) bound to hen egg lysozyme variant HEL2X-flex (mutations R21Q, R73E, C76S, and C94S)
6P4B · HYHEL10 Fab light chain: “HYHEL10 Fab variant HYHEL10-4X (heavy chain mutations L4F, Y33H, S56N, and Y58F) bound to hen egg lysozyme…”. X-ray diffraction, 1 ligand (CL), 12 pockets (best druggability 0.66). MolNFT v1 #159887 on…
- PDB
- 6P4B
- Type
- protein
- Length
- 1,086 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HYHEL10 Fab light chain; HYHEL10 Fab heavy chain; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- A0A0E4B213, P00698
- Ligands
- CL
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | HYHEL10 Fab light chain | protein | 210 | 7% helix, 51% strand | A0A0E4B213 |
| H | HYHEL10 Fab heavy chain | protein | 205 | 6% helix, 54% strand | — |
| C, D | Lysozyme C (EC 3.2.1.17) | protein | 129 | 41% helix, 11% strand | P00698 |
| A | HYHEL10 Fab light chain | protein | 209 | 6% helix, 52% strand | A0A0E4B213 |
| B | HYHEL10 Fab heavy chain | protein | 204 | 7% helix, 52% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 9 copies · chains L, H, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.66 | 0.74 | 80 | empty |
| 2 | 610 | 0.62 | 0.74 | 62 | empty |
| 3 | 238 | 0.60 | 0.80 | 37 | empty |
| 4 | 176 | 0.54 | 0.80 | 29 | empty |
| 5 | 244 | 0.50 | 0.75 | 38 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1675 Ų buried · 13 hydrogen bonds · protein-protein
- L–H · 1662 Ų buried · 13 hydrogen bonds · protein-protein
- H–C · 585 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 546 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 405 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6P4B · HyHEL10 fab variant HyHEL10-4x (heavy chain mutations L4F, Y33H, S56N, and Y58F) bound to… · the same entry in another collection · chain L against L, 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 A0A0E4B213
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 6P4B · PDBe 6P4B · UniProt A0A0E4B213 · UniProt P00698
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