3O2W | pdb_00003o2w

Crystal structure of the 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab in complex with a 39A11 transition state analog

PDB DOI: https://doi.org/10.2210/pdb3O2W/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-22 Released: 2011-07-20
Deposition Author(s): Verdino, P., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.248 (Depositor), 0.250 (DCC)
R-Value Work:
0.207 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab in complex with a 39A11 transition state analog

Verdino, P., Aldag, C., Jonsson, S., Hilvert, D., Wilson, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 51.54 kDa
Atom Count: 3,611
Modeled Residue Count: 432
Deposited Residue Count: 446
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric antibody Fab 1E9, light chain	A [auth L]	219	Mus musculus, Homo sapiens This entity is chimeric	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
Chimeric antibody Fab 1E9, heavy chain	B [auth H]	227	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O2W Query on O2W Download Ideal Coordinates CCD File SDF format, chain C [auth L] MOL2 format, chain C [auth L] mmCIF format, chain C [auth L]	C [auth L]	methyl ({[(3aR,4R,7R,7aR)-2-(4-aminophenyl)-1,3-dioxooctahydro-4H-4,7-ethanoisoindol-4-yl]carbamoyl}oxy)acetate C₂₀ H₂₃ N₃ O₆ PWUNEFYJETTWLK-KCQBUTHOSA-N		Interactions Focus chain C [auth L] Interactions & Density Focus chain C [auth L]
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain S [auth H] SDF format, chain T [auth H] SDF format, chain U [auth H] MOL2 format, chain S [auth H] MOL2 format, chain T [auth H] MOL2 format, chain U [auth H] mmCIF format, chain S [auth H] mmCIF format, chain T [auth H] mmCIF format, chain U [auth H]	S [auth H], T [auth H], U [auth H]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H] Interactions & Density Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain D [auth L] SDF format, chain E [auth L] SDF format, chain F [auth L] SDF format, chain G [auth L] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain P [auth H] SDF format, chain Q [auth H] SDF format, chain R [auth H] MOL2 format, chain D [auth L] MOL2 format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain G [auth L] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H] MOL2 format, chain R [auth H] mmCIF format, chain D [auth L] mmCIF format, chain E [auth L] mmCIF format, chain F [auth L] mmCIF format, chain G [auth L] mmCIF format, chain N [auth H] mmCIF format, chain O [auth H] mmCIF format, chain P [auth H] mmCIF format, chain Q [auth H] mmCIF format, chain R [auth H]	D [auth L] E [auth L] F [auth L] G [auth L] N [auth H] D [auth L], E [auth L], F [auth L], G [auth L], N [auth H], O [auth H], P [auth H], Q [auth H], R [auth H]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth H] Interactions & Density Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth L] SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain L SDF format, chain M [auth L] SDF format, chain V [auth H] SDF format, chain W [auth H] SDF format, chain X [auth H] SDF format, chain Y [auth H] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain V [auth H] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth H] mmCIF format, chain H [auth L] mmCIF format, chain I [auth L] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain L mmCIF format, chain M [auth L] mmCIF format, chain V [auth H] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth H]	H [auth L] I [auth L] J [auth L] K [auth L] L H [auth L], I [auth L], J [auth L], K [auth L], L, M [auth L], V [auth H], W [auth H], X [auth H], Y [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth L] 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 V [auth H] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth H] Interactions & Density Focus chain H [auth L] 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 V [auth H] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.248 (Depositor), 0.250 (DCC)
R-Value Work: 0.207 (Depositor), 0.210 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.203	α = 90
b = 128.203	β = 90
c = 92.144	γ = 120

Software Package:

Software Name	Purpose
BOS	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Verdino, P.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary