MolNFT v1 · #72606 · protein
Crystal structure of O-succinylhomoserine sulfhydrylase from mycobacterium tuberculosis covalently bound to pyridoxal-5-phosphate
3NDN: “Crystal structure of O-succinylhomoserine sulfhydrylase from mycobacterium tuberculosis covalently bound to…”. X-ray diffraction, 14 pockets (best druggability 0.77). MolNFT v1 #72606 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3NDN
- Type
- protein
- Length
- 1,604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-succinylhomoserine sulfhydrylase
- EC
- 4.2.99.-
- UniProt
- P95199
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | O-succinylhomoserine sulfhydrylase (EC 4.2.99.-) | protein | 401 | 42% helix, 15% strand | P95199 |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.77 | 0.81 | 90 | empty |
| 2 | 728 | 0.76 | 0.81 | 94 | empty |
| 3 | 79 | 0.75 | 0.98 | 39 | empty |
| 4 | 666 | 0.74 | 0.80 | 77 | empty |
| 5 | 447 | 0.73 | 0.83 | 56 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2935 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 2795 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 1801 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1750 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1115 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 3NDN · Crystal structure of O-succinylhomoserine sulfhydrylase from Mycobacterium tuberculosis… · 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 P95199
- Elsewhere: RCSB PDB 3NDN · PDBe 3NDN · UniProt P95199
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