1X1K | pdb_00001x1k

Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4

PDB DOI: https://doi.org/10.2210/pdb1X1K/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Saimiriine herpesvirus 2
Mutation(s): No

Deposited: 2005-04-05 Released: 2005-06-14
Deposition Author(s): Jiravanichanun, N., Hongo, C., Wu, G., Noguchi, K., Okuyama, K., Nishino, N., Silva, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.232 (Depositor)
R-Value Work:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Unexpected puckering of hydroxyproline in the guest triplets, hyp-pro-gly and pro-allohyp-gly sandwiched between pro-pro-gly sequence

Jiravanichanun, N., Hongo, C., Wu, G., Noguchi, K., Okuyama, K., Nishino, N., Silva, T.

(2005) Chembiochem 6: 1184-1187

PubMed: 15929160 Search on PubMed
DOI: https://doi.org/10.1002/cbic.200500055
Primary Citation Related Structures:
1X1K

Organizational Affiliation

Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan. natthac@cc.tuat.ac.jp

Macromolecule Content

Total Structure Weight: 14.04 kDa
Atom Count: 1,276
Modeled Residue Count: 163
Deposited Residue Count: 165
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4	A, B, C, D, E	27	N/A	Mutation(s): 0
UniProt
Find proteins for Q80BK4 (Saimiriine herpesvirus 2) Explore Q80BK4 Go to UniProtKB: Q80BK4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q80BK4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Host-guest peptide (Pro-Pro-Gly)4-(Pro-alloHyp-Gly)-(Pro-Pro-Gly)4	F	30	N/A	Mutation(s): 0
UniProt
Find proteins for Q80BK4 (Saimiriine herpesvirus 2) Explore Q80BK4 Go to UniProtKB: Q80BK4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q80BK4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP Query on HYP	A, B, C, D, E	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.232 (Depositor)
R-Value Work: 0.170 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.445	α = 90
b = 26.039	β = 89.98
c = 80.309	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
CrystalClear	data reduction
CrystalClear	data scaling
SHELX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-06-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-06-14
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description