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SMTL ID : 6yb6.1

Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x DPN: D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative(Non-covalent)

DPN.1:

10 residues within 4Å:

Chain B: Y.47, E.94, N.95, L.96, I.179, W.227, G.228, E.229
Ligands: PRO.8, OJK.9

4 PLIP interactions:

4 interactions with chain B

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

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

NA.2:	4 residues within 4Å: Chain B: K.174, D.175, T.177, R.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174
NA.3:	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:G.235, B:G.238

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4:	7 residues within 4Å: Chain B: L.130, Q.131, A.132, I.167, V.168, R.170, F.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.170
DMS.7:	6 residues within 4Å: Chain B: R.89, N.91, D.97, R.98, R.180, T.182 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.91, B:D.97, B:R.98, B:R.180 Water bridges: B:R.180 Salt bridges: B:D.97

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

NAG.5:

4 residues within 4Å:

Chain B: L.46, P.48, N.53, W.92

3 PLIP interactions:

3 interactions with chain B

Hydrophobic interactions: B:L.46, B:P.48
Hydrogen bonds: B:N.53

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

PO4.6:

4 residues within 4Å:

Chain B: E.124, T.125, S.128, F.215

2 PLIP interactions:

2 interactions with chain B

Water bridges: B:S.128, B:S.128

1 x PRO: PROLINE(Non-covalent)

PRO.8:

8 residues within 4Å:

Chain B: H.43, Y.47, W.50, L.96, S.226, W.227
Ligands: DPN.1, OJK.9

3 PLIP interactions:

3 interactions with chain B,

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

1 x OJK: 2-(aminomethyl)-5-chloranyl-benzene-1,4-diol(Non-covalent)

OJK.9:

14 residues within 4Å:

Chain B: H.43, D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, G.230, C.231
Ligands: DPN.1, PRO.8

5 PLIP interactions:

5 interactions with chain B

Hydrogen bonds: B:S.226, B:S.226
Water bridges: B:S.226, B:G.230
Halogen bonds: B:D.199

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Sandner, A. et al., Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c). To be published

Release Date

2021-03-31

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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Background

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