1HHC | pdb_00001hhc

Crystal structure of Decaplanin - space group P21, second form

PDB DOI: https://doi.org/10.2210/pdb1HHC/pdb

Classification: ANTIBIOTIC
Organism(s): uncultured actinomycete
Mutation(s): No

Deposited: 2000-12-22 Released: 2005-07-11
Deposition Author(s): Lehmann, C., Vertessy, L., Sheldrick, G.M., Dauter, Z., Dauter, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free:
0.264 (Depositor)
R-Value Work:
0.205 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Literature

Structures of Four Crystal Forms of Decaplanin

Lehmann, C., Debreczeni, J.E., Bunkoczi, G., Dauter, M., Dauter, Z., Vertesy, L., Sheldrick, G.M.

(2003) Helvetica Chim Acta 86: 1478

DOI: https://doi.org/10.1002/HLCA.200390131

Macromolecule Content

Total Structure Weight: 6.99 kDa
Atom Count: 629
Modeled Residue Count: 28
Deposited Residue Count: 28
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DECAPLANIN	A, B, C, D	7	uncultured actinomycete	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-rhamnopyranose-(1-2)-beta-D-glucopyranose	E, F, G, H	2		N/A	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G13233ZQ GlyCosmos: G13233ZQ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain J [auth A] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth A] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth A]	J [auth A], M [auth C], O [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain J [auth A] Focus chain M [auth C] Focus chain O [auth D]
ERE Query on ERE Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A], K [auth B], L [auth C], N [auth D]	4-epi-vancosamine C₇ H₁₅ N O₃ OIJZDPGKNVKVBL-VZFHVOOUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D]

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3FG Query on 3FG	A, B, C, D	L-PEPTIDE LINKING	C₈ H₉ N O₄		--
GHP Query on GHP	A, B, C, D	D-PEPTIDE LINKING	C₈ H₉ N O₃		--
MLU Query on MLU	A, B, C, D	D-PEPTIDE LINKING	C₇ H₁₅ N O₂		--
OMX Query on OMX	A, B, C, D	L-PEPTIDE LINKING	C₉ H₁₁ N O₄		TYR
OMZ Query on OMZ	A, B, C, D	D-PEPTIDE LINKING	C₉ H₁₀ Cl N O₄		--

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000207 Query on PRD_000207	A, B, C, D	Decaplanin	Glycopeptide / Antibiotic		Interactions Focus chain A Focus chain B Focus chain C Focus chain D Interactions & Density Focus chain A Focus chain B Focus chain C Focus chain D

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000207 Query on PRD_000207	E, F, G, H	Decaplanin	Glycopeptide / Antibiotic		Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free: 0.264 (Depositor)
R-Value Work: 0.205 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.945	α = 90
b = 31.908	β = 109.87
c = 34.735	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SAINT	data reduction
SADABS	data scaling
EPMR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-07-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-07-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
Version 1.2: 2012-07-25
Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description
Version 1.3: 2012-11-30
Changes: Other
Version 1.4: 2013-05-01
Changes: Non-polymer description
Version 2.0: 2019-04-24
Changes: Data collection, Derived calculations, Other, Polymer sequence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 3.1: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary