2HOD

Crystal Structure of Fragment D from Human Fibrinogen Complexed with Gly-hydroxyPro-Arg-Pro-amide

PDB DOI: https://doi.org/10.2210/pdb2HOD/pdb

Classification: BLOOD CLOTTING/PEPTIDE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2006-07-14 Released: 2007-05-29
Deposition Author(s): Doolittle, R.F., Kollman, J.M., Chen, A., Pandi, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.347 (Depositor), 0.340 (DCC)
R-Value Work:
0.268 (Depositor), 0.260 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 342.82 kDa
Atom Count: 22,278
Modelled Residue Count: 2,771
Deposited Residue Count: 2,992
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen alpha chain	A, D, G, J	87	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02671 (Homo sapiens) Explore P02671 Go to UniProtKB: P02671
PHAROS: P02671 GTEx: ENSG00000171560
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02671
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen beta chain	B, E, H, K	328	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02675 (Homo sapiens) Explore P02675 Go to UniProtKB: P02675
PHAROS: P02675 GTEx: ENSG00000171564
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02675
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain E Focus chain H Focus chain K	Go to GlyGen: P02675-1
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen, gamma polypeptide	C, F, I, L	323	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02679 (Homo sapiens) Explore P02679 Go to UniProtKB: P02679
PHAROS: P02679 GTEx: ENSG00000171557
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02679
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Gly-hydroxyPro-Arg-Pro-amide peptide ligand	M, N, O, P, Q M, N, O, P, Q, R, S, T	5	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain EA [auth K] SDF format, chain U [auth B] SDF format, chain X [auth E] MOL2 format, chain BA [auth H] MOL2 format, chain EA [auth K] MOL2 format, chain U [auth B] MOL2 format, chain X [auth E] mmCIF format, chain BA [auth H] mmCIF format, chain EA [auth K] mmCIF format, chain U [auth B] mmCIF format, chain X [auth E]	BA [auth H], EA [auth K], U [auth B], X [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth H] Focus chain EA [auth K] Focus chain U [auth B] Focus chain X [auth E] Interactions & Density Focus chain BA [auth H] Focus chain EA [auth K] Focus chain U [auth B] Focus chain X [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain CA [auth H] SDF format, chain DA [auth I] SDF format, chain FA [auth K] SDF format, chain GA [auth K] SDF format, chain HA [auth L] SDF format, chain V [auth B] SDF format, chain W [auth C] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain CA [auth H] MOL2 format, chain DA [auth I] MOL2 format, chain FA [auth K] MOL2 format, chain GA [auth K] MOL2 format, chain HA [auth L] MOL2 format, chain V [auth B] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain CA [auth H] mmCIF format, chain DA [auth I] mmCIF format, chain FA [auth K] mmCIF format, chain GA [auth K] mmCIF format, chain HA [auth L] mmCIF format, chain V [auth B] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	AA [auth F] CA [auth H] DA [auth I] FA [auth K] GA [auth K] AA [auth F], CA [auth H], DA [auth I], FA [auth K], GA [auth K], HA [auth L], V [auth B], W [auth C], Y [auth E], Z [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth H] Focus chain DA [auth I] Focus chain FA [auth K] Focus chain GA [auth K] Focus chain HA [auth L] Focus chain V [auth B] Focus chain W [auth C] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth H] Focus chain DA [auth I] Focus chain FA [auth K] Focus chain GA [auth K] Focus chain HA [auth L] Focus chain V [auth B] Focus chain W [auth C] Focus chain Y [auth E] Focus chain Z [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP Query on HYP	M, N, O, P, Q M, N, O, P, Q, R, S, T	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.347 (Depositor), 0.340 (DCC)
R-Value Work: 0.268 (Depositor), 0.260 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.647	α = 90
b = 47.069	β = 90.06
c = 431.46	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-05-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-05-29
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary