8CN9

Factor VII binding Fab of the bispecific antibody HMB-001 in complex with Factor VII

PDB DOI: https://doi.org/10.2210/pdb8CN9/pdb

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-02-22 Released: 2023-12-27
Deposition Author(s): Schluckebier, G., Johansson, E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.356
R-Value Work: 0.303
R-Value Observed: 0.305

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A bispecific antibody approach for the potential prophylactic treatment of inherited bleeding disorders

Gandhi, P.S., Zivkovic, M., Oestergaard, H., Bonde, A.C., Loevgreen, M.N., Schluckebier, G., Johansson, E., Rea, C.J., Soerensen, B., Schutgens, R.E., Urbanus, R.T., Faber, J.H.

(2023) Nat Cardiovasc Res

Macromolecule Content

Total Structure Weight: 446.75 kDa
Atom Count: 29,516
Modelled Residue Count: 3,818
Deposited Residue Count: 4,056
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	A, F, K, P	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	B, G, L, Q	220	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	C, H, M, R	254	Homo sapiens	Mutation(s): 0 Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709
PHAROS: P08709 GTEx: ENSG00000057593
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	D, I, N, S	107	Homo sapiens	Mutation(s): 0 Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709
PHAROS: P08709 GTEx: ENSG00000057593
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	E, J, O, T	219	Homo sapiens	Mutation(s): 0 Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726 Go to UniProtKB: P13726
PHAROS: P13726 GTEx: ENSG00000117525
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13726
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain HA [auth S] SDF format, chain W [auth D] MOL2 format, chain AA [auth I] MOL2 format, chain HA [auth S] MOL2 format, chain W [auth D]	AA [auth I], HA [auth S], W [auth D]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain AA [auth I] Focus chain HA [auth S] Focus chain W [auth D] Interactions & Density Focus chain AA [auth I] Focus chain HA [auth S] Focus chain W [auth D]
CS Query on CS Download Ideal Coordinates CCD File SDF format, chain EA [auth P] MOL2 format, chain EA [auth P]	EA [auth P]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain EA [auth P] Interactions & Density Focus chain EA [auth P]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth K] SDF format, chain CA [auth M] SDF format, chain DA [auth M] SDF format, chain FA [auth R] SDF format, chain GA [auth R] SDF format, chain U [auth A] SDF format, chain V [auth C] SDF format, chain X [auth F] SDF format, chain Y [auth H] SDF format, chain Z [auth H] MOL2 format, chain BA [auth K] MOL2 format, chain CA [auth M] MOL2 format, chain DA [auth M] MOL2 format, chain FA [auth R] MOL2 format, chain GA [auth R] MOL2 format, chain U [auth A] MOL2 format, chain V [auth C] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth H] MOL2 format, chain Z [auth H]	BA [auth K] CA [auth M] DA [auth M] FA [auth R] GA [auth R] BA [auth K], CA [auth M], DA [auth M], FA [auth R], GA [auth R], U [auth A], V [auth C], X [auth F], Y [auth H], Z [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth K] Focus chain CA [auth M] Focus chain DA [auth M] Focus chain FA [auth R] Focus chain GA [auth R] Focus chain U [auth A] Focus chain V [auth C] Focus chain X [auth F] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth K] Focus chain CA [auth M] Focus chain DA [auth M] Focus chain FA [auth R] Focus chain GA [auth R] Focus chain U [auth A] Focus chain V [auth C] Focus chain X [auth F] Focus chain Y [auth H] Focus chain Z [auth H]