3AOG | pdb_00003aog

Crystal structure of glutamate dehydrogenase (GdhB) from Thermus thermophilus (Glu bound form)

PDB DOI: https://doi.org/10.2210/pdb3AOG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB27
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-28 Released: 2011-09-07
Deposition Author(s): Tomita, T., Kuzuyama, T., Nishiyama, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.277 (Depositor), 0.270 (DCC)
R-Value Work:
0.226 (Depositor), 0.220 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

An unique allosteric regulation revealed by crystal structure of hetero-hexameric glutamate dehydrogenase from Thermus thermophilus

Tomita, T., Kuzuyama, T., Nishiyama, M.

To be published.

Macromolecule Content

Total Structure Weight: 580.35 kDa
Atom Count: 40,944
Modeled Residue Count: 5,047
Deposited Residue Count: 5,280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	440	Thermus thermophilus HB27	Mutation(s): 0 Gene Names: TT_C1211 EC: 1.4.1.3
UniProt
Find proteins for Q72IC1 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72IC1 Go to UniProtKB: Q72IC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q72IC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLU Query on GLU Download Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain XA [auth L] SDF format, chain X [auth D] SDF format, chain WA [auth L] SDF format, chain W [auth D] SDF format, chain UA [auth K] SDF format, chain U [auth C] SDF format, chain TA [auth K] SDF format, chain T [auth C] SDF format, chain R [auth B] SDF format, chain QA [auth J] SDF format, chain Q [auth B] SDF format, chain PA [auth J] SDF format, chain N [auth A] SDF format, chain MA [auth I] SDF format, chain M [auth A] SDF format, chain LA [auth I] SDF format, chain JA [auth H] SDF format, chain IA [auth H] SDF format, chain GA [auth G] SDF format, chain FA [auth G] SDF format, chain CA [auth F] SDF format, chain BA [auth F] SDF format, chain AA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain XA [auth L] MOL2 format, chain X [auth D] MOL2 format, chain WA [auth L] MOL2 format, chain W [auth D] MOL2 format, chain UA [auth K] MOL2 format, chain U [auth C] MOL2 format, chain TA [auth K] MOL2 format, chain T [auth C] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth I] MOL2 format, chain JA [auth H] MOL2 format, chain IA [auth H] MOL2 format, chain GA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain XA [auth L] mmCIF format, chain X [auth D] mmCIF format, chain WA [auth L] mmCIF format, chain W [auth D] mmCIF format, chain UA [auth K] mmCIF format, chain U [auth C] mmCIF format, chain TA [auth K] mmCIF format, chain T [auth C] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth J] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth J] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth I] mmCIF format, chain JA [auth H] mmCIF format, chain IA [auth H] mmCIF format, chain GA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth F] CA [auth F] FA [auth G] GA [auth G] AA [auth E], BA [auth F], CA [auth F], FA [auth G], GA [auth G], IA [auth H], JA [auth H], LA [auth I], M [auth A], MA [auth I], N [auth A], PA [auth J], Q [auth B], QA [auth J], R [auth B], T [auth C], TA [auth K], U [auth C], UA [auth K], W [auth D], WA [auth L], X [auth D], XA [auth L], Z [auth E]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain R [auth B] Focus chain T [auth C] Focus chain TA [auth K] Focus chain U [auth C] Focus chain UA [auth K] Focus chain W [auth D] Focus chain WA [auth L] Focus chain X [auth D] Focus chain XA [auth L] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain R [auth B] Focus chain T [auth C] Focus chain TA [auth K] Focus chain U [auth C] Focus chain UA [auth K] Focus chain W [auth D] Focus chain WA [auth L] Focus chain X [auth D] Focus chain XA [auth L] Focus chain Z [auth E]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain VA [auth K] SDF format, chain V [auth C] SDF format, chain RA [auth J] SDF format, chain OA [auth I] SDF format, chain O [auth A] SDF format, chain NA [auth I] SDF format, chain HA [auth G] SDF format, chain DA [auth F] MOL2 format, chain Y [auth D] MOL2 format, chain VA [auth K] MOL2 format, chain V [auth C] MOL2 format, chain RA [auth J] MOL2 format, chain OA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain HA [auth G] MOL2 format, chain DA [auth F] mmCIF format, chain Y [auth D] mmCIF format, chain VA [auth K] mmCIF format, chain V [auth C] mmCIF format, chain RA [auth J] mmCIF format, chain OA [auth I] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth I] mmCIF format, chain HA [auth G] mmCIF format, chain DA [auth F]	DA [auth F] HA [auth G] NA [auth I] O [auth A] OA [auth I] DA [auth F], HA [auth G], NA [auth I], O [auth A], OA [auth I], RA [auth J], V [auth C], VA [auth K], Y [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain DA [auth F] Focus chain HA [auth G] Focus chain NA [auth I] Focus chain O [auth A] Focus chain OA [auth I] Focus chain RA [auth J] Focus chain V [auth C] Focus chain VA [auth K] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth F] Focus chain HA [auth G] Focus chain NA [auth I] Focus chain O [auth A] Focus chain OA [auth I] Focus chain RA [auth J] Focus chain V [auth C] Focus chain VA [auth K] Focus chain Y [auth D]
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain YA [auth L] SDF format, chain SA [auth J] SDF format, chain S [auth B] SDF format, chain P [auth A] SDF format, chain KA [auth H] SDF format, chain EA [auth F] MOL2 format, chain YA [auth L] MOL2 format, chain SA [auth J] MOL2 format, chain S [auth B] MOL2 format, chain P [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain EA [auth F] mmCIF format, chain YA [auth L] mmCIF format, chain SA [auth J] mmCIF format, chain S [auth B] mmCIF format, chain P [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain EA [auth F]	EA [auth F] KA [auth H] P [auth A] S [auth B] SA [auth J] EA [auth F], KA [auth H], P [auth A], S [auth B], SA [auth J], YA [auth L]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain EA [auth F] Focus chain KA [auth H] Focus chain P [auth A] Focus chain S [auth B] Focus chain SA [auth J] Focus chain YA [auth L] Interactions & Density Focus chain EA [auth F] Focus chain KA [auth H] Focus chain P [auth A] Focus chain S [auth B] Focus chain SA [auth J] Focus chain YA [auth L]