2VD3 | pdb_00002vd3

The structure of histidine inhibited HisG from Methanobacterium thermoautotrophicum

PDB DOI: https://doi.org/10.2210/pdb2VD3/pdb

Classification: TRANSFERASE
Organism(s): Methanothermobacter thermautotrophicus str. Delta H
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2007-09-28 Released: 2008-11-04
Deposition Author(s): Lohkamp, B., Schweikert, T., Lapthorn, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.287 (Depositor), 0.270 (DCC)
R-Value Work:
0.226 (Depositor), 0.220 (DCC)
R-Value Observed:
0.231 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The Structure of Histidine Inhibited Hisg from Methanobacterium Thermoautotrophicum

Lohkamp, B., Schweikert, T., Lapthorn, A.J.

To be published.

Macromolecule Content

Total Structure Weight: 64.44 kDa
Atom Count: 4,575
Modeled Residue Count: 577
Deposited Residue Count: 578
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP PHOSPHORIBOSYLTRANSFERASE	A, B	289	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0 EC: 2.4.2.17
UniProt
Find proteins for O27550 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O27550 Go to UniProtKB: O27550
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O27550
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HIS Query on HIS Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain C [auth A] mmCIF format, chain Q [auth B]	C [auth A], Q [auth B]	HISTIDINE C₆ H₁₀ N₃ O₂ HNDVDQJCIGZPNO-YFKPBYRVSA-O		Interactions Focus chain C [auth A] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain Q [auth B]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain N [auth A] SDF format, chain P [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A]	CA [auth B], DA [auth B], EA [auth B], N [auth A], P [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain N [auth A] Focus chain P [auth A] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain N [auth A] Focus chain P [auth A]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain T [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain T [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain T [auth B]	E [auth A], F [auth A], T [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain T [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain R [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain R [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	D [auth A] G [auth A] H [auth A] I [auth A] R [auth B] D [auth A], G [auth A], H [auth A], I [auth A], R [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain R [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain R [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain S [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] J [auth A] K [auth A] L [auth A] AA [auth B], BA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], S [auth B], Y [auth B], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.287 (Depositor), 0.270 (DCC)
R-Value Work: 0.226 (Depositor), 0.220 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.103	α = 90
b = 112.103	β = 90
c = 247.622	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-11-04

Deposition Author(s):

Lohkamp, B.

Schweikert, T.

Lapthorn, A.J.

Revision History (Full details and data files)

Version 1.0: 2008-11-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other, Refinement description