SMTL ID : 3na9.1

Crystal structure of Fab15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: D.151, H.189 Ligands: ACT.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.151, A:H.189, ACT.4 ZN.2: 3 residues within 4Å: Chain A: N.137, N.138 Chain B: H.172 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.172, H2O.11, H2O.15 ZN.3: 3 residues within 4Å: Chain A: E.123 Chain B: H.220 Ligands: ACT.5 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:H.220, A:E.123, ACT.5, H2O.8 ZN.6: 5 residues within 4Å: Chain A: C.214 Chain B: H.221, H.222, H.225 Ligands: ACT.10 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: A:C.214, B:H.221, B:H.225, ACT.10 ZN.7: 2 residues within 4Å: Chain B: H.222, H.224 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.222, B:H.224 ZN.8: 3 residues within 4Å: Chain B: S.136, H.221, H.223 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.223, H2O.11, H2O.18 ZN.9: 2 residues within 4Å: Chain B: D.73, S.75 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.73, B:S.75, H2O.15

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 4 residues within 4Å: Chain A: D.151, K.188, H.189 Ligands: ZN.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.189 ACT.5: 8 residues within 4Å: Chain A: S.121, D.122, E.123 Chain B: H.220, H.221, H.222, H.225 Ligands: ZN.3 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.222, A:D.122 Salt bridges: B:H.220 ACT.10: 7 residues within 4Å: Chain A: C.214 Chain B: S.136, H.221, H.222, H.223, H.225 Ligands: ZN.6 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:C.214 Hydrophobic interactions: B:H.223 Hydrogen bonds: B:S.136 Salt bridges: B:H.221, B:H.225 ACT.11: 4 residues within 4Å: Chain B: A.133, L.197, V.219, H.221 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.133

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 11 residues within 4Å: Chain A: Q.160, S.162, S.176, S.177, T.178 Chain B: F.174, P.175, V.177, S.185, L.186, S.187 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.160, A:S.162, A:T.178, B:F.174, B:S.187 Water bridges: A:S.176 GOL.13: 5 residues within 4Å: Chain B: Y.32, W.33, E.99, Y.101, D.106 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.33, B:E.99, B:D.106 Water bridges: B:Y.101, B:Y.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, J. et al., Co-evolution of antibody stability and Vk CDR-L3 canonical structure. To be Published

Release Date

2010-08-18

Peptides

Fab15 light chain: A
Fab15 heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Fab15 light chain

Fab15 heavy chain

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