6VMK | pdb_00006vmk

Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12

PDB DOI: https://doi.org/10.2210/pdb6VMK/pdb

Classification: HYDROLASE/IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Cricetulus griseus, Escherichia coli
Mutation(s): No

Deposited: 2020-01-28 Released: 2021-02-03
Deposition Author(s): Wu, P., Harris, S.F., Eigenbrot, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.01 Å
R-Value Free:
0.215 (Depositor), 0.210 (DCC)
R-Value Work:
0.174 (Depositor), 0.170 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12

Dion, M., Wu, P., Morando, A., Bullen, G., Shatz, W., Harris, S.F., Eigenbrot, C., Loyet, K.M., Yadav, D., Tassew, N., Booler, H., Scheer, J., Kelley, R.F., Tesar, D.B.

To be published.

Macromolecule Content

Total Structure Weight: 1,146.02 kDa
Atom Count: 80,635
Modelled Residue Count: 10,464
Deposited Residue Count: 10,640
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement factor D	A [auth W] BA [auth d] D [auth C] EA [auth g] G [auth F] A [auth W], BA [auth d], D [auth C], EA [auth g], G [auth F], HA [auth j], J [auth I], KA [auth m], M [auth N], NA [auth p], P [auth Q], QA [auth s], S [auth T], TA [auth v], V [auth X], Y [auth a]	228	Homo sapiens	Mutation(s): 0 Gene Names: CFD, DF, PFD EC: 3.4.21.46
UniProt & NIH Common Fund Data Resources
Find proteins for P00746 (Homo sapiens) Explore P00746 Go to UniProtKB: P00746
PHAROS: P00746 GTEx: ENSG00000197766
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00746
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 Y49R light chain	B [auth L] CA [auth b] E [auth A] FA [auth e] H [auth D] B [auth L], CA [auth b], E [auth A], FA [auth e], H [auth D], IA [auth h], K [auth G], LA [auth k], N [auth J], OA [auth n], Q [auth O], RA [auth q], T [auth R], UA [auth t], W [auth U], Z [auth Y]	214	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Y49R heavy chain	AA [auth Z] C [auth M] DA [auth c] F [auth B] GA [auth f] AA [auth Z], C [auth M], DA [auth c], F [auth B], GA [auth f], I [auth E], JA [auth i], L [auth H], MA [auth l], O [auth K], PA [auth o], R [auth P], SA [auth r], U [auth S], VA [auth u], X [auth V]	223	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain DB [auth N] SDF format, chain FB [auth Q] SDF format, chain JB [auth X] SDF format, chain NB [auth g] SDF format, chain PB [auth j] SDF format, chain RB [auth m] SDF format, chain TB [auth p] SDF format, chain VB [auth s] SDF format, chain XA [auth W] SDF format, chain XB [auth v] SDF format, chain ZA [auth C] SDF format, chain HB [auth T] MOL2 format, chain DB [auth N] MOL2 format, chain FB [auth Q] MOL2 format, chain JB [auth X] MOL2 format, chain NB [auth g] MOL2 format, chain PB [auth j] MOL2 format, chain RB [auth m] MOL2 format, chain TB [auth p] MOL2 format, chain VB [auth s] MOL2 format, chain XA [auth W] MOL2 format, chain XB [auth v] MOL2 format, chain ZA [auth C] MOL2 format, chain HB [auth T] mmCIF format, chain DB [auth N] mmCIF format, chain FB [auth Q] mmCIF format, chain JB [auth X] mmCIF format, chain NB [auth g] mmCIF format, chain PB [auth j] mmCIF format, chain RB [auth m] mmCIF format, chain TB [auth p] mmCIF format, chain VB [auth s] mmCIF format, chain XA [auth W] mmCIF format, chain XB [auth v] mmCIF format, chain ZA [auth C] mmCIF format, chain HB [auth T]	DB [auth N] FB [auth Q] HB [auth T] JB [auth X] NB [auth g] DB [auth N], FB [auth Q], HB [auth T], JB [auth X], NB [auth g], PB [auth j], RB [auth m], TB [auth p], VB [auth s], XA [auth W], XB [auth v], ZA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DB [auth N] Focus chain FB [auth Q] Focus chain HB [auth T] Focus chain JB [auth X] Focus chain NB [auth g] Focus chain PB [auth j] Focus chain RB [auth m] Focus chain TB [auth p] Focus chain VB [auth s] Focus chain XA [auth W] Focus chain XB [auth v] Focus chain ZA [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BB [auth I] SDF format, chain CB [auth N] SDF format, chain GB [auth T] SDF format, chain IB [auth X] SDF format, chain KB [auth a] SDF format, chain LB [auth d] SDF format, chain MB [auth g] SDF format, chain OB [auth j] SDF format, chain QB [auth m] SDF format, chain SB [auth p] SDF format, chain UB [auth s] SDF format, chain WA [auth W] SDF format, chain WB [auth v] SDF format, chain YA [auth C] SDF format, chain EB [auth Q] MOL2 format, chain AB [auth F] MOL2 format, chain BB [auth I] MOL2 format, chain CB [auth N] MOL2 format, chain GB [auth T] MOL2 format, chain IB [auth X] MOL2 format, chain KB [auth a] MOL2 format, chain LB [auth d] MOL2 format, chain MB [auth g] MOL2 format, chain OB [auth j] MOL2 format, chain QB [auth m] MOL2 format, chain SB [auth p] MOL2 format, chain UB [auth s] MOL2 format, chain WA [auth W] MOL2 format, chain WB [auth v] MOL2 format, chain YA [auth C] MOL2 format, chain EB [auth Q] mmCIF format, chain AB [auth F] mmCIF format, chain BB [auth I] mmCIF format, chain CB [auth N] mmCIF format, chain GB [auth T] mmCIF format, chain IB [auth X] mmCIF format, chain KB [auth a] mmCIF format, chain LB [auth d] mmCIF format, chain MB [auth g] mmCIF format, chain OB [auth j] mmCIF format, chain QB [auth m] mmCIF format, chain SB [auth p] mmCIF format, chain UB [auth s] mmCIF format, chain WA [auth W] mmCIF format, chain WB [auth v] mmCIF format, chain YA [auth C] mmCIF format, chain EB [auth Q]	AB [auth F] BB [auth I] CB [auth N] EB [auth Q] GB [auth T] AB [auth F], BB [auth I], CB [auth N], EB [auth Q], GB [auth T], IB [auth X], KB [auth a], LB [auth d], MB [auth g], OB [auth j], QB [auth m], SB [auth p], UB [auth s], WA [auth W], WB [auth v], YA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain BB [auth I] Focus chain CB [auth N] Focus chain EB [auth Q] Focus chain GB [auth T] Focus chain IB [auth X] Focus chain KB [auth a] Focus chain LB [auth d] Focus chain MB [auth g] Focus chain OB [auth j] Focus chain QB [auth m] Focus chain SB [auth p] Focus chain UB [auth s] Focus chain WA [auth W] Focus chain WB [auth v] Focus chain YA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.01 Å
R-Value Free: 0.215 (Depositor), 0.210 (DCC)
R-Value Work: 0.174 (Depositor), 0.170 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 263.704	α = 90
b = 301.454	β = 90
c = 458.842	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-02-03

Deposition Author(s):

Wu, P.

Harris, S.F.

Eigenbrot, C.

Revision History (Full details and data files)

Version 1.0: 2021-02-03
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

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Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12

Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

Entity Groups

Sequence Annotations

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Entity ID: 3

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

6VMK | pdb_00006vmk