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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wwPDB Validation 3D Report Full Report

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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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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

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

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.