SMTL ID : 9f23.2 (1 other biounit)

DARPin eGFP complex DP2 (2G156)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: 2-[[(2S)-2-oxidanylpropoxy]methyl]-2-[[(2S)-2-[(2S)-2-oxidanylpropoxy]propoxy]methyl]propane-1,3-diol

01.1: 8 residues within 4Å: Chain A: E.98, R.99, T.100, K.110, T.111, Y.185, Q.187 Ligands: PXN.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.187 Hydrogen bonds: A:T.100, A:T.100, A:T.100 Water bridges: A:K.110, A:K.110

1 x PXN: (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol(Non-covalent)

PXN.2: 8 residues within 4Å: Chain A: D.24, G.25, K.110, R.112, E.127, L.128, K.129 Ligands: 01.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.127 Water bridges: A:G.25, A:G.25

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: R.112, A.113, E.114, R.125, E.127 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.112, A:R.112 EDO.4: 3 residues within 4Å: Chain A: K.57, D.219 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.57 Water bridges: A:D.219, A:H.220 EDO.5: 6 residues within 4Å: Chain A: K.212, E.216, K.217, R.218, H.220 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.217 Water bridges: A:H.220 EDO.6: 5 residues within 4Å: Chain A: E.22, D.24, R.125, I.126 Ligands: EDO.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.24, A:R.125, A:I.126, A:I.126 EDO.7: 6 residues within 4Å: Chain A: K.104, D.105, D.106, G.137, N.138, Q.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.138, A:Q.180 Water bridges: A:Q.180 EDO.9: 5 residues within 4Å: Chain B: G.72, Q.101, D.102, K.103 Ligands: TRS.14 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain B: D.5, G.7, K.8, A.34, D.35, D.36 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.35 EDO.11: 4 residues within 4Å: Chain B: K.106, D.110, I.113, D.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.110, B:D.114

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

NA.8: 4 residues within 4Å: Chain A: P.61, W.62, P.63, Y.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.62 Water bridges: A:V.60, A:W.62, A:H.142

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.12: 7 residues within 4Å: Chain A: E.39, K.46 Chain B: L.11, E.12, D.36, I.40, L.45 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.39, A:K.46, B:D.36 TRS.13: 3 residues within 4Å: Chain B: E.21, I.24, L.25 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.9, B:K.9, B:N.28 TRS.14: 5 residues within 4Å: Chain B: T.68, D.69, L.70, G.72 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.68, B:T.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Winkelvoss, D. et al., DARPin eGFP complex DP2 (2G156). To Be Published

Release Date

2024-10-23

Peptides

Green fluorescent protein: A
DARPin DP2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Green fluorescent protein

DARPin DP2

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