MolNFT v1 · #124205 · protein
X-ray structure of kdna, 8-amino-3,8-dideoxy-alpha-D-manno- octulosonate transaminase, from shewanella oneidensis in the presence of the external aldimine with plp and glutamate
5K8B: “X-ray structure of kdna, 8-amino-3,8-dideoxy-alpha-D-manno- octulosonate transaminase, from shewanella…”. X-ray diffraction, 3 ligands (PDG, NA, CL). MolNFT v1 #124205 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5K8B
- Type
- protein
- Length
- 1,576 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- Q8EEB1
- Ligands
- PDG, NA, CL
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | — | protein | 394 | — | Q8EEB1 |
Ligands and binding sites
- PDG · N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-glutamic acid · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5K8B · X-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase… · the same entry in another collection · chain B against B, TM-score 1.00
- Q8EEB1 · AlphaFold monomer V2.0 prediction for 8-amino-3,8-dideoxy-alpha-D- manno-octulosonate… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8EEB1
- Elsewhere: RCSB PDB 5K8B · PDBe 5K8B · UniProt Q8EEB1
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