1QD3

HIV-1 TAR RNA/NEOMYCIN B COMPLEX

PDB DOI: https://doi.org/10.2210/pdb1QD3/pdb
NAKB: 1QD3

Classification: RNA
Organism(s): Human immunodeficiency virus 1
Mutation(s): No

Deposited: 1999-07-07 Released: 2000-07-12
Deposition Author(s): Faber, C., Sticht, H., Roesch, P.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 17
Selection Criteria: LOWEST ENERGY, AGREEMENT WITH EXPERIMENTAL DATA

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 9.96 kDa
Atom Count: 657
Modelled Residue Count: 29
Deposited Residue Count: 29
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
HIV-1 TAR RNA	A	29	Human immunodeficiency virus 1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2,6-diamino-2,6-dideoxy-beta-L-idopyranose-(1-3)-alpha-D-ribofuranose	B	2		N/A	Interactions Focus chain B
Glycosylation Resources
GlyTouCan: G90578XL GlyCosmos: G90578XL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BDG Query on BDG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose C₆ H₁₄ N₂ O₄ SQTHUUHOUPJYLK-UKFBFLRUSA-N		Interactions Focus chain C [auth A]
CYY Query on CYY Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	2-DEOXYSTREPTAMINE C₆ H₁₄ N₂ O₃ DTFAJAKTSMLKAT-JDCCYXBGSA-N		Interactions Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
RIB	PDBBind: 1QD3	Kd: 5900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 17
Selection Criteria: LOWEST ENERGY, AGREEMENT WITH EXPERIMENTAL DATA

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-07-12

Deposition Author(s):

Faber, C.

Sticht, H.

Roesch, P.

Revision History (Full details and data files)

Version 1.0: 2000-07-12
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Structure summary

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Help and Resources

1QD3

HIV-1 TAR RNA/NEOMYCIN B COMPLEX

Entity ID: 1

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)