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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P07204 New Search
13PDB entries
18Biological assembly
18chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1ADX FIFTH EGF-LIKE DOMAIN OF THROMBOMODULIN (TMEGF5), NMR, 14 STRUCTURES Deposited 1997-02-18 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 405–444（40 aa） Fragment：FIFTH EGF-LIKE DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K
Resolution not provided
1DQB NMR STRUCTURE OF THROMBOMODULIN EGF(4-5) Deposited 2000-01-03 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 344–426（83 aa） Fragment：THE FOURTH AND FIFTH EGF-LIKE DOMAINS
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SOLUTION NMR
NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 1mM TM45 U-15N; 90% H2O, 10% D2O, pH 6.5 | 90% H2O/10% D2O
NMR sample composition 1mM TM45; 100% D2O | 100% D2O
Resolution not provided
1DX5 Crystal structure of the thrombin-thrombomodulin complex Deposited 1999-12-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: tetrameric（4） Review required
Chain I 363–480（118 aa） Fragment：EGF-LIKE DOMAINS 4 - 6
Mutation：YES FMT FORMIC ACID × 1 CA CALCIUM ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE
Resolution 2.30 Å R-free 0.241
1DX5 Crystal structure of the thrombin-thrombomodulin complex Deposited 1999-12-20 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: tetrameric（4） Review required
Chain J 363–480（118 aa） Fragment：EGF-LIKE DOMAINS 4 - 6
Mutation：YES FMT FORMIC ACID × 1 CA CALCIUM ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE
Resolution 2.30 Å R-free 0.241
1DX5 Crystal structure of the thrombin-thrombomodulin complex Deposited 1999-12-20 Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: tetrameric（4） Review required
Chain K 363–480（118 aa） Fragment：EGF-LIKE DOMAINS 4 - 6
Mutation：YES FMT FORMIC ACID × 1 CA CALCIUM ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE
Resolution 2.30 Å R-free 0.241
1DX5 Crystal structure of the thrombin-thrombomodulin complex Deposited 1999-12-20 Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: tetrameric（4） Review required
Chain L 363–480（118 aa） Fragment：EGF-LIKE DOMAINS 4 - 6
Mutation：YES FMT FORMIC ACID × 2 CA CALCIUM ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE
Resolution 2.30 Å R-free 0.241
1EGT THROMBIN-BOUND STRUCTURE OF AN EGF SUBDOMAIN FROM HUMAN THROMBOMODULIN DETERMINED BY TRANSFERRED NUCLEAR OVERHAUSER EFFECTS Deposited 1994-10-12 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 427–444（18 aa）
Mutation：DEL(ILE 420) No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1FGD EPIDERMAL GROWTH FACTOR (EGF) SUBDOMAIN OF HUMAN THROMBOMODULIN (NMR, 11 STRUCTURES) Deposited 1995-11-28 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 427–444（18 aa） Fragment：C-TERMINAL SUBDOMAIN, RESIDUES 409 - 426, OF 5TH EPIDERMAL GROWTH FACTOR (EGF)
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1FGE EPIDERMAL GROWTH FACTOR (EGF) SUBDOMAIN OF HUMAN THROMBOMODULIN (NMR, 14 STRUCTURES) Deposited 1995-11-28 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 425–444（20 aa） Fragment：C-TERMINAL SUBDOMAIN, RESIDUES 407 - 426, OF 5TH EPIDERMAL GROWTH FACTOR (EGF)
Mutation：C409A No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1HLT THE STRUCTURE OF A NONADECAPEPTIDE OF THE FIFTH EGF DOMAIN OF THROMBOMODULIN COMPLEXED WITH THROMBIN Deposited 1994-08-28 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain R 426–444（19 aa）
Not recorded 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1TMR THE STRUCTURE OF A 19 RESIDUE FRAGMENT FROM THE C-LOOP OF THE FOURTH EPIDERMAL GROWTH FACTOR-LIKE DOMAIN OF THROMBOMODULIN Deposited 1994-05-20 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 389–407（19 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1ZAQ FOURTH EGF-LIKE DOMAIN OF THROMBOMODULIN, NMR, 12 STRUCTURES Deposited 1995-09-09 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 364–407（44 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2ADX FIFTH EGF-LIKE DOMAIN OF THROMBOMODULIN (TMEGF5), NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-02-18 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 405–444（40 aa） Fragment：FIFTH EGF-LIKE DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K
Resolution not provided
3GIS Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin Deposited 2009-03-06 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain X 363–483（121 aa） Fragment：Thrombomodulin EGF domains 4-5-6, UNP residues 363-483
Mutation：M388L,R456G,H457Q SO4 SULFATE ION × 7 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；294 K；0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION
Resolution 2.40 Å R-free 0.259
3GIS Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin Deposited 2009-03-06 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain Y 363–483（121 aa） Fragment：Thrombomodulin EGF domains 4-5-6, UNP residues 363-483
Mutation：M388L,R456G,H457Q SO4 SULFATE ION × 5 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；294 K；0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION
Resolution 2.40 Å R-free 0.259
3GIS Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin Deposited 2009-03-06 Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain Z 363–483（121 aa） Fragment：Thrombomodulin EGF domains 4-5-6, UNP residues 363-483
Mutation：M388L,R456G,H457Q SO4 SULFATE ION × 3 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；294 K；0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION
Resolution 2.40 Å R-free 0.259
5TO3 Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to PPACK Deposited 2016-10-16 Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 363–483（121 aa）
Mutation：W215A, E217A 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 K POTASSIUM ION × 1 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100 mM HEPES and 20% PEG 8000
Resolution 2.34 Å R-free 0.255
7T4R CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with THBD and neutralizing fabs MSL-109 and 13H11 Deposited 2021-12-10 Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric（19） Consistent with protein count
Chain A 1–516（516 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot for 3.5s before plunging
Resolution 3.30 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.