3QRG | pdb_00003qrg

Crystal structure of antiRSVF Fab B21m

PDB DOI: https://doi.org/10.2210/pdb3QRG/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2011-02-17 Released: 2011-08-10
Deposition Author(s): Luo, J., Tsui, P., Lewandowski, F., Spurlino, J., Vecchio, F.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.185 (Depositor), 0.180 (DCC)
R-Value Work:
0.161 (Depositor), 0.150 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure anti-RSV Fab B21m

Luo, J., Tsui, P., Lewandowski, F., Spurlino, J., Vecchio, F.D.

To be published.

Macromolecule Content

Total Structure Weight: 50.74 kDa
Atom Count: 4,215
Modeled Residue Count: 437
Deposited Residue Count: 445
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	A [auth L]	218	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain Fd fragment	B [auth H]	227	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain Z [auth H] MOL2 format, chain Z [auth H] mmCIF format, chain Z [auth H]	Z [auth H]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain Z [auth H] Interactions & Density Focus chain Z [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain X [auth H] SDF format, chain W [auth H] SDF format, chain V [auth H] SDF format, chain U [auth H] SDF format, chain T [auth H] SDF format, chain S [auth H] SDF format, chain R [auth H] SDF format, chain N [auth L] SDF format, chain M [auth L] SDF format, chain L SDF format, chain K [auth L] SDF format, chain J [auth L] SDF format, chain I [auth L] MOL2 format, chain Y [auth H] MOL2 format, chain X [auth H] MOL2 format, chain W [auth H] MOL2 format, chain V [auth H] MOL2 format, chain U [auth H] MOL2 format, chain T [auth H] MOL2 format, chain S [auth H] MOL2 format, chain R [auth H] MOL2 format, chain N [auth L] MOL2 format, chain M [auth L] MOL2 format, chain L MOL2 format, chain K [auth L] MOL2 format, chain J [auth L] MOL2 format, chain I [auth L] mmCIF format, chain Y [auth H] mmCIF format, chain X [auth H] mmCIF format, chain W [auth H] mmCIF format, chain V [auth H] mmCIF format, chain U [auth H] mmCIF format, chain T [auth H] mmCIF format, chain S [auth H] mmCIF format, chain R [auth H] mmCIF format, chain N [auth L] mmCIF format, chain M [auth L] mmCIF format, chain L mmCIF format, chain K [auth L] mmCIF format, chain J [auth L] mmCIF format, chain I [auth L]	I [auth L] J [auth L] K [auth L] L M [auth L] I [auth L], J [auth L], K [auth L], L, M [auth L], N [auth L], R [auth H], S [auth H], T [auth H], U [auth H], V [auth H], W [auth H], X [auth H], Y [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain R [auth H] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth H] Interactions & Density Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain R [auth H] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth H] SDF format, chain P [auth H] SDF format, chain O [auth H] SDF format, chain H [auth L] SDF format, chain G [auth L] SDF format, chain F [auth L] SDF format, chain E [auth L] SDF format, chain D [auth L] SDF format, chain C [auth L] MOL2 format, chain Q [auth H] MOL2 format, chain P [auth H] MOL2 format, chain O [auth H] MOL2 format, chain H [auth L] MOL2 format, chain G [auth L] MOL2 format, chain F [auth L] MOL2 format, chain E [auth L] MOL2 format, chain D [auth L] MOL2 format, chain C [auth L] mmCIF format, chain Q [auth H] mmCIF format, chain P [auth H] mmCIF format, chain O [auth H] mmCIF format, chain H [auth L] mmCIF format, chain G [auth L] mmCIF format, chain F [auth L] mmCIF format, chain E [auth L] mmCIF format, chain D [auth L] mmCIF format, chain C [auth L]	C [auth L] D [auth L] E [auth L] F [auth L] G [auth L] C [auth L], D [auth L], E [auth L], F [auth L], G [auth L], H [auth L], O [auth H], P [auth H], Q [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth L] Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Interactions & Density Focus chain C [auth L] Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	B [auth H]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.185 (Depositor), 0.180 (DCC)
R-Value Work: 0.161 (Depositor), 0.150 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.412	α = 90
b = 166.412	β = 90
c = 166.412	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNX	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-08-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-10
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 2.0: 2019-12-25
Changes: Derived calculations, Polymer sequence
Version 2.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary