Research workbench
NB36 SER85CYS with hg bound
Analyse NB36 SER85CYS with hg bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NML
- Type
- protein
- Length
- 1,128 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody NB36 SER85CYS
- Ligands
- HG
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody NB36 SER85CYS | protein | 120 | 8% helix, 45% strand | — |
| B, C, E, F | Nanobody NB36 SER85CYS | protein | 118 | 8% helix, 47% strand | — |
| D, H | Nanobody NB36 SER85CYS | protein | 117 | 8% helix, 46% strand | — |
| G | Nanobody NB36 SER85CYS | protein | 110 | 9% helix, 49% strand | — |
| I | Nanobody NB36 SER85CYS | protein | 117 | 11% helix, 45% strand | — |
| J | Nanobody NB36 SER85CYS | protein | 75 | 8% helix, 49% strand | — |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 9 copies · chains A, G, B, C, D, F, H
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, E, H, I
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 | 929 | 0.75 | 0.79 | 104 | empty |
| 2 | 370 | 0.68 | 0.82 | 35 | empty |
| 3 | 283 | 0.60 | 0.79 | 31 | empty |
| 4 | 163 | 0.55 | 0.80 | 25 | empty |
| 5 | 269 | 0.53 | 0.76 | 38 | empty |
Interfaces
14 interfaces between chains.
- H–I · 920 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 905 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 551 Ų buried · 8 hydrogen bonds · protein-protein
- G–J · 489 Ų buried · 7 hydrogen bonds · protein-protein
- A–G · 358 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5NML · Nb36 Ser85Cys with Hg bound · 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
- Elsewhere: RCSB PDB 5NML · PDBe 5NML
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