9C2K | pdb_00009c2k

The crystal structure of HIV-1 Rev Response Element Stem-Loop II in complex with a Fab

PDB DOI: https://doi.org/10.2210/pdb9C2K/pdb
NAKB: 9C2K

Classification: RNA
Organism(s): Homo sapiens, Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-31 Released: 2025-05-28
Deposition Author(s): Ojha, M., Koirala, D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.265 (Depositor), 0.266 (DCC)
R-Value Work:
0.205 (Depositor), 0.208 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of HIV-1 RRE SL2 in complex with Fab BL3-6

Ojha, M., Koirala, D.

To be published.

Macromolecule Content

Total Structure Weight: 144.82 kDa
Atom Count: 10,271
Modeled Residue Count: 1,026
Deposited Residue Count: 1,040
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BL3-6 Fab heavy chain	A [auth H], C [auth A]	233	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BL3-6 Fab light chain	B [auth L], D [auth B]	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Rev Response Element	E [auth R], F [auth C]	72	Human immunodeficiency virus 1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain K [auth L] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Y [auth R] MOL2 format, chain BA [auth C] MOL2 format, chain K [auth L] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth R] mmCIF format, chain BA [auth C] mmCIF format, chain K [auth L] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth R]	BA [auth C], K [auth L], R [auth B], S [auth B], Y [auth R]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth C] Focus chain K [auth L] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth R] Interactions & Density Focus chain BA [auth C] Focus chain K [auth L] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth R]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth R] SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain L SDF format, chain M [auth L] SDF format, chain N [auth L] SDF format, chain O [auth L] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain AA [auth R] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain N [auth L] MOL2 format, chain O [auth L] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain AA [auth R] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain L mmCIF format, chain M [auth L] mmCIF format, chain N [auth L] mmCIF format, chain O [auth L] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	AA [auth R] G [auth H] H I [auth H] J [auth H] AA [auth R], G [auth H], H, I [auth H], J [auth H], L, M [auth L], N [auth L], O [auth L], P [auth A], Q [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth R] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain AA [auth R] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Z [auth R] MOL2 format, chain Z [auth R] mmCIF format, chain Z [auth R]	Z [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Z [auth R] Interactions & Density Focus chain Z [auth R]