1TB6

2.5A Crystal Structure of the Antithrombin-Thrombin-Heparin Ternary Complex

Structural Biology Knowledgebase: 1TB6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.208

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1TB6

Classification: HYDROLASE / BLOOD CLOTTING

Total Structure Weight: 92152.72

Macromolecule Entities
Molecule Chains Length Organism Details
thrombin L 49 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: thrombin light chain
Gene Name(s): F2 Gene View
thrombin H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: thrombin heavy chain, serine protease
Mutation: S195A
Gene Name(s): F2 Gene View
Antithrombin-III I 432 Homo sapiens Mutation: S137A, V317C, T401C
Gene Name(s): SERPINC1 Gene View AT3 PRO0309

Small Molecules
Ligands 15 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GU4
Query on GU4

I 2,3,4,6-TETRA-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE
C6 H8 O18 S4
SPIXVQOXHJQNTH-DVKNGEFBSA-J
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GU6
Query on GU6

I 2,3,6-TRI-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE
C6 H12 O15 S3
GRHWGVDHRAZFMQ-DVKNGEFBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GU0
Query on GU0

I 2,3,6-TRI-O-SULFONATO-ALPHA-L-GALACTOPYRANOSE
C6 H9 O15 S3
GRHWGVDHRAZFMQ-VFUOTHLCSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GU3
Query on GU3

I methyl 3-O-methyl-2,6-di-O-sulfo-alpha-D- glucopyranoside
C8 H16 O12 S2
GFHCIIGKYHICQU-CBQIKETKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GU5
Query on GU5

I 2,3-DI-O-METHYL-6-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE
C8 H15 O9 S
SYRNRUURZIIPLL-IINKRSELSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GU8
Query on GU8

I 2,3,6-TRI-O-METHYL-BETA-D-GLUCOPYRANOSE
C9 H18 O6
LXJBARMBDDODTG-SRBFPGQKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GU9
Query on GU9

I 2,3,6-TRI-O-METHYL-ALPHA-D-GLUCOPYRANOSE
C9 H18 O6
LXJBARMBDDODTG-MSMGWUHYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GU1
Query on GU1

I 2,3-DI-O-METHYL-BETA-D-GLUCOPYRANURONIC ACID
C8 H14 O7
YEGNNGDFCAGXPA-GRJZWZNASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GU2
Query on GU2

I 2,3-DI-O-METHYL-ALPHA-L-IDOPYRANURONIC ACID
C8 H14 O7
YEGNNGDFCAGXPA-OHZVEFKRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NDG
Query on NDG

H, I 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

H, I N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

I BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

I ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

H ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

H, I (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.208
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 88.41 α = 90.00
b = 88.40 β = 90.00
c = 117.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-05-19
  • Released Date: 2004-08-17
  • Deposition author(s): Li, W., Johnson, D.J., Esmon, C.T., Huntington, J.A.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4