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SMTL ID : 6yhg.1

Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

PO4.1:

7 residues within 4Å:

Chain B: R.89, N.91, N.95, D.97, R.98, R.180, T.182

11 PLIP interactions:

11 interactions with chain B

Hydrogen bonds: B:N.91, B:D.97, B:D.97
Water bridges: B:R.89, B:E.94, B:R.98, B:R.180, B:R.180, B:R.180
Salt bridges: B:R.98, B:R.180

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

NA.2:	5 residues within 4Å: Chain B: D.232, R.233, D.234, G.235, K.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:R.197, B:G.238
NA.3:	1 residues within 4Å: Chain B: F.215 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.215

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

NAG.4:

3 residues within 4Å:

Chain B: L.46, P.48, N.53

1 PLIP interactions:

1 interactions with chain B

Hydrophobic interactions: B:P.48

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5:

10 residues within 4Å:

Chain B: L.27, C.28, H.43, W.50, K.52, E.202, G.203, S.205
Ligands: PRO.7, SZ4.8

5 PLIP interactions:

4 interactions with chain B, 1 Ligand-Ligand interactions

Hydrogen bonds: B:L.27, B:G.203, B:S.205, B:S.205, P.7

1 x DPN: D-PHENYLALANINE(Non-covalent)

DPN.6:

10 residues within 4Å:

Chain B: Y.47, E.94, N.95, L.96, I.179, W.227, G.228, E.229
Ligands: PRO.7, SZ4.8

5 PLIP interactions:

5 interactions with chain B

Hydrophobic interactions: B:I.179, B:W.227
Hydrogen bonds: B:G.228, B:G.228
Water bridges: B:G.230

1 x PRO: PROLINE(Non-covalent)

PRO.7:

9 residues within 4Å:

Chain B: H.43, Y.47, W.50, L.96, S.226, W.227
Ligands: GOL.5, DPN.6, SZ4.8

3 PLIP interactions:

3 interactions with chain B,

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96

1 x SZ4: 1-(3-methoxyphenyl)methanamine(Non-covalent)

SZ4.8:

16 residues within 4Å:

Chain B: H.43, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, G.230, G.238, F.239, Y.240
Ligands: GOL.5, DPN.6, PRO.7

4 PLIP interactions:

4 interactions with chain B

Hydrophobic interactions: B:V.225
Hydrogen bonds: B:H.43, B:S.226, B:S.226

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Sandner, A. et al., Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a). To be published

Release Date

2021-04-07

Peptides

Prothrombin: A
Prothrombin: B
Hirudin variant-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Prothrombin

Prothrombin

Hirudin variant-2

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Cartoon
Tube
Trace
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Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
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