5B4P | pdb_00005b4p

Complex structure of human C5a and its binding repebody

PDB DOI: https://doi.org/10.2210/pdb5B4P/pdb

Classification: SIGNALING PROTEIN/MEMBRANE PROTEIN
Organism(s): synthetic construct, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-04-12 Released: 2017-04-12
Deposition Author(s): Kim, H.-S., Choi, J.M., Hwang, D.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.310 (Depositor), 0.311 (DCC)
R-Value Work:
0.272 (Depositor), 0.268 (DCC)
R-Value Observed:
0.274 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5B4P

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

Literature

Complex structure of human C5a and its binding repebody

Kim, H.-S., Choi, J.M., Hwang, D.E.

To be published.

Macromolecule Content

Total Structure Weight: 76.08 kDa
Atom Count: 5,157
Modeled Residue Count: 658
Deposited Residue Count: 672
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
repebody	A, C	261	synthetic construct	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C5a anaphylatoxin	B, D	75	Homo sapiens	Mutation(s): 0 Gene Names: C5, CPAMD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens) Explore P01031 Go to UniProtKB: P01031
PHAROS: P01031 GTEx: ENSG00000106804
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01031
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain J [auth B]	F [auth A] G [auth A] H [auth A] J [auth B] K [auth C] F [auth A], G [auth A], H [auth A], J [auth B], K [auth C], L [auth C], M [auth C], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.310 (Depositor), 0.311 (DCC)
R-Value Work: 0.272 (Depositor), 0.268 (DCC)
R-Value Observed: 0.274 (Depositor)

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.837	α = 90
b = 87.553	β = 90
c = 188.392	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-04-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-04-12
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Structure summary

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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.