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SMTL ID : 5e8e.1

Crystal structure of thrombin bound to an exosite 1-specific IgA Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1:

3 residues within 4Å:

Chain A: N.28, S.30, R.92

No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-SIA.2:

3 residues within 4Å:

Chain C: L.46, N.53, T.55

No protein-ligand interaction detected (PLIP)

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3:	6 residues within 4Å: Chain A: A.9, Y.87, G.101, G.102 Chain B: Q.39, K.43 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.9, A:Y.87, A:K.104
PEG.6:	7 residues within 4Å: Chain C: V.168, R.170, C.173, F.186, C.187, H.242, R.245 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.170, C:C.187, C:H.242, C:R.245
PEG.13:	3 residues within 4Å: Chain C: Y.220 Chain D: E.6, C.9 No protein-ligand interaction detected (PLIP)

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4:	5 residues within 4Å: Chain B: D.183, S.185, G.186, D.187, L.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.185, B:D.187, B:L.188
PO4.8:	7 residues within 4Å: Chain C: D.6, L.144, K.154, P.157, S.158, V.159, Q.161 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.6, C:D.6, C:S.158, C:S.158, C:V.159, C:Q.161 Water bridges: C:D.6 Salt bridges: C:K.154
PO4.9:	4 residues within 4Å: Chain C: W.50, E.202, G.203 Ligands: 0G6.12 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.203 Water bridges: C:K.52, C:K.52, C:K.52, C:E.202, C:E.202
PO4.10:	4 residues within 4Å: Chain C: N.91, D.97, R.98, R.180 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.91, C:D.97 Water bridges: C:R.180, C:R.180 Salt bridges: C:R.98, C:R.180
PO4.11:	3 residues within 4Å: Chain C: R.123, F.244, K.248 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.123 Salt bridges: C:R.123, C:K.248

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5:

5 residues within 4Å:

Chain C: H.87, P.88, R.89, K.248, W.249

7 PLIP interactions:

7 interactions with chain C

Water bridges: C:K.248, C:K.252, C:K.252, C:K.252
Salt bridges: C:H.87, C:R.89, C:K.252

1 x NA: SODIUM ION(Non-functional Binders)

NA.7:

3 residues within 4Å:

Chain C: D.232, R.233, K.236

4 PLIP interactions:

4 interactions with chain C

Hydrogen bonds: C:Y.190, C:K.236
Water bridges: C:G.235, C:G.238

1 x 0G6: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide(Covalent)

0G6.12:

20 residues within 4Å:

Chain C: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, G.203, D.204, S.205, S.226, W.227, G.228, G.230, C.231, G.238
Ligands: PO4.9

18 PLIP interactions:

18 interactions with chain C

Hydrophobic interactions: C:Y.47, C:W.50, C:I.179, C:W.227
Hydrogen bonds: C:A.200, C:G.203, C:D.204, C:S.205, C:S.226, C:G.228, C:G.228, C:G.230
Water bridges: C:E.202, C:E.202, C:W.227, C:D.232, C:Y.240
Salt bridges: C:D.199

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Baglin, T.P. et al., Discovery and characterization of an antibody directed against exosite I of thrombin. J.Thromb.Haemost. (2016)

Release Date

2015-10-28

Peptides

IGA FAB LIGHT CHAIN: A
IGA FAB HEAVY CHAIN: B
THROMBIN HEAVY CHAIN: C
THROMBIN LIGHT CHAIN: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

IGA FAB LIGHT CHAIN

IGA FAB HEAVY CHAIN

THROMBIN HEAVY CHAIN

THROMBIN LIGHT CHAIN

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