3ez5
Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA , dCTP, and zinc (closed form).
1. Protein Identity and Related Structures Protein Identity & Related Structures
No usable UniProt protein identity is available for this entry.
The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.
Assembly Composition of the Current Entry
| Assembly | Physical composition | Protein state | 蛋白 / DNA / RNA / 其他Polymer | Data consistency |
|---|---|---|---|---|
| 1 | Protein–DNA | Monomer | 1 / 2 / 0 / 1 | Review required |
| 2 | Protein–DNA | Monomer | 1 / 2 / 0 / 1 | Review required |
The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.
2. Structure Basics 2. Structure Basics
| Entry ID entry_id | 3ez5 |
| Deposition date deposition_date | 2008-10-22 |
| Structure title title | Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA , dCTP, and zinc (closed form). |
| Keywords keywords | protein-DNA complex, TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA |
| Experimental Method method | X-RAY DIFFRACTION |
3. Official assembly/model SAXS Official SAXS Profiles
This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.
3ez5__assembly_2__model_1
Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)
3ez5__assembly_2__model_1 | I(q)
3ez5__assembly_2__model_1 | P(r) · Pending
| Rg（Guinier） | 26.57 Å |
| Rg (electron density) | 25.97 Å |
| Total Rg | 26.65 Å |
| Atom count | 5130 |
| Residues | 600 |
| Excluded volume | 90302 ų |
| Maximum q | 0.500 Å⁻¹ |
4. Crystallography and Experiment 4. Crystallography & Experiment
5. Entities and Polymers Entities & Polymers (8)
6. Fold Classification (SCOP + CATH) 13 domains
SCOP 2.08 (5 domains)
| Domain ID domain_id | d3ez5a1 |
| Class class | c — Alpha and beta proteins (a/b) |
| Fold Fold fold | c.55 — Ribonuclease H-like motif |
| Superfamily Superfamily superfamily | c.55.3 — Ribonuclease H-like |
| Family Family family | c.55.3.5 — DnaQ-like 3'-5' exonuclease |
| Domain ID domain_id | d3ez5a2 |
| Class class | e — Multi-domain proteins (alpha and beta) |
| Fold Fold fold | e.8 — DNA/RNA polymerases |
| Superfamily Superfamily superfamily | e.8.1 — DNA/RNA polymerases |
| Family Family family | e.8.1.1 — DNA polymerase I |
| Domain ID domain_id | d3ez5a3 |
| Class class | l — Artifacts |
| Fold Fold fold | l.1 — Tags |
| Superfamily Superfamily superfamily | l.1.1 — Tags |
| Family Family family | l.1.1.1 — Tags |
| Domain ID domain_id | d3ez5d1 |
| Class class | c — Alpha and beta proteins (a/b) |
| Fold Fold fold | c.55 — Ribonuclease H-like motif |
| Superfamily Superfamily superfamily | c.55.3 — Ribonuclease H-like |
| Family Family family | c.55.3.5 — DnaQ-like 3'-5' exonuclease |
| Domain ID domain_id | d3ez5d2 |
| Class class | e — Multi-domain proteins (alpha and beta) |
| Fold Fold fold | e.8 — DNA/RNA polymerases |
| Superfamily Superfamily superfamily | e.8.1 — DNA/RNA polymerases |
| Family Family family | e.8.1.1 — DNA polymerase I |
CATH v4.4 (8 domains)
| Domain ID domain_id | 3ez5A01 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 30 — 2-Layer Sandwich |
| Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| Homologous superfamily homologous superfamily | 10 — Ribonuclease H-like superfamily/Ribonuclease H |
| Domain ID domain_id | 3ez5A02 |
| Class class | 1 — Mainly Alpha |
| Architecture architecture | 20 — Up-down Bundle |
| Topology topology | 1060 — Taq DNA Polymerase; Chain T, domain 4 |
| Homologous superfamily homologous superfamily | 10 — Taq DNA Polymerase; Chain T, domain 4 |
| Domain ID domain_id | 3ez5A03 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 30 — 2-Layer Sandwich |
| Topology topology | 70 — Alpha-Beta Plaits |
| Homologous superfamily homologous superfamily | 370 — |
| Domain ID domain_id | 3ez5A04 |
| Class class | 1 — Mainly Alpha |
| Architecture architecture | 10 — Orthogonal Bundle |
| Topology topology | 150 — DNA polymerase; domain 1 |
| Homologous superfamily homologous superfamily | 20 — 5' to 3' exonuclease, C-terminal subdomain |
| Domain ID domain_id | 3ez5D01 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 30 — 2-Layer Sandwich |
| Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| Homologous superfamily homologous superfamily | 10 — Ribonuclease H-like superfamily/Ribonuclease H |
| Domain ID domain_id | 3ez5D02 |
| Class class | 1 — Mainly Alpha |
| Architecture architecture | 20 — Up-down Bundle |
| Topology topology | 1060 — Taq DNA Polymerase; Chain T, domain 4 |
| Homologous superfamily homologous superfamily | 10 — Taq DNA Polymerase; Chain T, domain 4 |
| Domain ID domain_id | 3ez5D03 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 30 — 2-Layer Sandwich |
| Topology topology | 70 — Alpha-Beta Plaits |
| Homologous superfamily homologous superfamily | 370 — |
| Domain ID domain_id | 3ez5D04 |
| Class class | 1 — Mainly Alpha |
| Architecture architecture | 10 — Orthogonal Bundle |
| Topology topology | 150 — DNA polymerase; domain 1 |
| Homologous superfamily homologous superfamily | 20 — 5' to 3' exonuclease, C-terminal subdomain |