SMTL ID : 6ss5.1

Structure of the arginase-2-inhibitory human antigen-binding fragment Fab C0020187

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

hetero-1-1-mer

Ligands

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 6 residues within 4Å: Chain A: K.225 Chain B: P.127, E.218, C.219, S.220 Ligands: EPE.6 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: F.31, T.32, Y.36 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: Y.36, R.104, A.105, D.106 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: S.6, V.7, V.104, F.105 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: S.122, V.123, V.210, K.212 Ligand excluded by PLIP

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 10 residues within 4Å: Chain A: V.97, Y.99, R.116, G.117, T.118, L.119 Chain B: Q.43, G.46, T.47, A.48 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.97 Hydrogen bonds: B:G.46 MPD.9: 10 residues within 4Å: Chain A: A.37, A.54, I.55, S.56, Y.63, L.103, A.105, L.109 Chain B: W.96, L.103 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.96, A:Y.63, A:L.103, A:L.109 MPD.10: 10 residues within 4Å: Chain A: G.46, K.47, G.48 Chain B: P.12, D.90, Y.92, G.107, G.108, T.109, K.110 No protein-ligand interaction detected (PLIP)

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 13 residues within 4Å: Chain A: A.148, G.173, V.174, H.175, V.192, T.194 Chain B: S.122, T.124, S.145, D.146, Q.175, S.176, N.177 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:G.173, A:T.194, B:S.145, B:Q.175, B:S.176, B:N.177 Water bridges: A:V.174, B:S.176 Salt bridges: B:D.146, B:D.146 EPE.6: 12 residues within 4Å: Chain A: C.227 Chain B: P.127, P.128, S.129, S.130, L.133, W.193, P.216, T.217, E.218, C.219 Ligands: CL.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.128, B:C.219 Water bridges: B:W.193

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 9 residues within 4Å: Chain B: E.88, T.112, V.113, G.115, Q.116, Y.148, K.174, N.178, Y.180 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.115, B:Q.116, B:Y.148, B:N.178 Water bridges: B:V.113, B:Y.148, B:K.174, B:Y.180 Salt bridges: B:K.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, D.T.Y. et al., Extensive sequence and structural evolution of Arginase 2 inhibitory antibodies enabled by an unbiased approach to affinity maturation. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-06-10

Peptides

Fab C0020187 heavy chain (IgG1): A
Fab C0020187 light chain (IgG1): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
HHH

B
LLL

Fab C0020187 heavy chain (IgG1)

Fab C0020187 light chain (IgG1)

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