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Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre

Source organism: Persephonella marina EX-H1
Biochemical function: metal ion binding
Biological process: not assigned
Cellular component: not assigned

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GO terms

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Sequence families

Pfam Protein families (Pfam)
PF13487
Domain description: HD domain
Occurring in:
  1. HD-GYP domain-containing protein
The deposited structure of PDB entry 4mdz contains 2 copies of Pfam domain PF13487 (HD domain) in HD-GYP domain-containing protein. Showing 1 copy in chain B.

PF01590
Domain description: GAF domain
Occurring in:
  1. HD-GYP domain-containing protein
The deposited structure of PDB entry 4mdz contains 2 copies of Pfam domain PF01590 (GAF domain) in HD-GYP domain-containing protein. Showing 1 copy in chain B.

InterPro InterPro annotations
IPR006674
Domain description: HD domain
Occurring in:
  1. HD-GYP domain-containing protein
IPR003607
Domain description: HD/PDEase domain
Occurring in:
  1. HD-GYP domain-containing protein
IPR003018
Domain description: GAF domain
Occurring in:
  1. HD-GYP domain-containing protein
IPR006675
Domain description: HDIG domain
Occurring in:
  1. HD-GYP domain-containing protein
IPR037522
Domain description: HD-GYP domain
Occurring in:
  1. HD-GYP domain-containing protein
IPR029016
Domain description: GAF-like domain superfamily
Occurring in:
  1. HD-GYP domain-containing protein

Structure domains

CATH CATH domains
1.10.3210.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Hypothetical protein af1432
Homology: Hypothetical protein af1432
Occurring in:
  1. HD-GYP domain-containing protein
The deposited structure of PDB entry 4mdz contains 2 copies of CATH domain 1.10.3210.10 (Hypothetical protein af1432) in HD-GYP domain-containing protein. Showing 1 copy in chain B.
3.30.450.40
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Beta-Lactamase
Homology: Beta-Lactamase
Occurring in:
  1. HD-GYP domain-containing protein
The deposited structure of PDB entry 4mdz contains 2 copies of CATH domain 3.30.450.40 (Beta-Lactamase) in HD-GYP domain-containing protein. Showing 1 copy in chain B.

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