7THI | pdb_00007thi

Human Bisphosphoglycerate Mutase complexed with 2-phosphoglycolate

PDB DOI: https://doi.org/10.2210/pdb7THI/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-11 Released: 2022-01-26
Deposition Author(s): Clark, K.L., Kulathila, R., Wright, K., Isome, Y., Sage, D., Yang, Y., Christodoulou, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free:
0.160 (Depositor), 0.160 (DCC)
R-Value Work:
0.134 (Depositor), 0.134 (DCC)
R-Value Observed:
0.136 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Human Bisphosphoglycerate Mutase complexed with 2-phosphoglycolate

Clark, K.L., Kulathila, R., Wright, K., Isome, Y., Sage, D., Yang, Y., Christodoulou, C.

To be published.

Macromolecule Content

Total Structure Weight: 62.55 kDa
Atom Count: 4,878
Modeled Residue Count: 509
Deposited Residue Count: 534
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bisphosphoglycerate mutase	A, B	267	Homo sapiens	Mutation(s): 0 Gene Names: BPGM EC: 5.4.2.4 (PDB Primary Data), 5.4.2.11 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P07738 (Homo sapiens) Explore P07738 Go to UniProtKB: P07738
PHAROS: P07738 GTEx: ENSG00000172331
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07738
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGA (Subject of Investigation/LOI) Query on PGA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	2-PHOSPHOGLYCOLIC ACID C₂ H₅ O₆ P ASCFNMCAHFUBCO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.160 (Depositor), 0.160 (DCC)
R-Value Work: 0.134 (Depositor), 0.134 (DCC)
R-Value Observed: 0.136 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.607	α = 90
b = 71.758	β = 90
c = 159.294	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-26

Deposition Author(s):

Christodoulou, C.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-01-26
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.