SMTL ID : 8sfx.2 (1 other biounit)

High Affinity nanobodies against GFP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: Y.150, N.197, H.198, Y.199, G.227 Ligands: MLT.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.198 GOL.2: 6 residues within 4Å: Chain A: F.98, F.99, K.100, D.101, D.102 Ligands: NA.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.100, A:D.101

1 x MLT: D-MALATE(Non-functional Binders)

MLT.3: 1 residues within 4Å: Ligands: GOL.1 No protein-ligand interaction detected (PLIP)

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

NA.4: 8 residues within 4Å: Chain A: D.102, F.129, K.130, G.133, N.134, I.135, L.136, G.137 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.102, A:G.133, A:I.135, A:L.136 Water bridges: A:N.134 NA.5: 7 residues within 4Å: Chain A: T.60, L.61, V.62, T.63, T.64, I.97, Y.105 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.61, A:T.63, A:T.63, A:T.64, A:T.64 Water bridges: A:V.62 NA.6: 6 residues within 4Å: Chain A: F.98, F.99, D.102, G.103, N.104 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.99, A:D.102 NA.7: 8 residues within 4Å: Chain A: X.66, V.67, Q.68, C.69, Y.91, Q.93, V.111, N.184 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.68, A:Y.91, A:Y.91, A:Q.93 NA.8: 2 residues within 4Å: Chain A: N.145, R.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.145, A:R.167, A:R.167 Water bridges: A:N.169 NA.9: 4 residues within 4Å: Chain A: V.12, D.37, Y.40, K.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.37, A:D.37 NA.10: 4 residues within 4Å: Chain A: P.57, W.58, P.59, Y.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.58 NA.11: 2 residues within 4Å: Chain A: G.34, E.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.34, A:E.35 NA.12: 2 residues within 4Å: Chain A: V.218, L.220 No protein-ligand interaction detected (PLIP) NA.13: 5 residues within 4Å: Chain A: P.14, I.15, E.33, G.34 Chain B: R.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.34 NA.16: 4 residues within 4Å: Chain A: N.211 Chain B: S.108, R.109, A.110 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.211, B:A.110 NA.17: 4 residues within 4Å: Chain B: R.109, A.110, Y.112, W.115 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.112, B:W.115

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

PO4.14: 3 residues within 4Å: Chain A: R.72, P.74, D.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.75 Salt bridges: A:R.72 PO4.15: 6 residues within 4Å: Chain A: P.14, E.114, G.115, D.116, T.117 Chain B: R.102 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.102 Hydrogen bonds: A:D.116, A:T.117, A:T.117 PO4.18: 3 residues within 4Å: Chain B: Q.40, R.46, R.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.40 Salt bridges: B:R.46, B:R.109 PO4.19: 2 residues within 4Å: Chain B: R.101, R.102 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:E.35, B:R.101, B:D.113 Salt bridges: B:R.101, B:R.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ketaren, N.E. et al., High Affinity nanobodies against GFP. To Be Published

Release Date

2024-05-22

Peptides

Green fluorescent protein: A
LaG21: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Green fluorescent protein

LaG21

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