SMTL ID : 6ss6.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-3-3-3-mer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 8 residues within 4Å: Chain A: H.99, W.120, D.122, H.124, D.126, D.230, E.275 Ligands: MN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.99, A:D.122, A:D.126, A:D.230 MN.2: 8 residues within 4Å: Chain A: H.99, D.122, A.123, H.124, D.230, D.232, E.275 Ligands: MN.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.122, A:H.124, A:D.230, A:D.232, A:D.232 MN.6: 8 residues within 4Å: Chain B: H.99, W.120, D.122, H.124, D.126, D.230, E.275 Ligands: MN.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.99, B:D.122, B:D.126, B:D.230 MN.7: 7 residues within 4Å: Chain B: D.122, A.123, H.124, D.230, D.232, E.275 Ligands: MN.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.122, B:H.124, B:D.230, B:D.232, B:D.232 MN.11: 8 residues within 4Å: Chain C: H.99, W.120, D.122, H.124, D.126, D.230, E.275 Ligands: MN.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.99, C:D.122, C:D.126, C:D.230 MN.12: 6 residues within 4Å: Chain C: D.122, A.123, H.124, D.230, D.232 Ligands: MN.11 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.122, C:H.124, C:D.230, C:D.232, C:D.232

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

SO4.3: 3 residues within 4Å: Chain A: R.203, L.204, R.212 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.199, R.203 Chain C: N.264 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: R.221, Q.222 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain B: R.203, L.204, R.212 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain B: R.221, Q.222 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain B: Q.304, H.310 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain C: R.203, L.204, R.212 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain C: R.69, L.157, P.158, G.159, F.160, S.161 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain C: R.221, Q.222 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain C: R.148, S.168, A.170, S.171, R.221, R.223 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain C: K.208, R.212 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: K.45, D.88, Y.90 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain D: R.23, K.80, Y.84 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain D: K.128, G.129 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain D: S.29, G.30 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain A: L.131 Chain C: T.318, P.319 Chain D: Y.36, R.104 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain A: L.131 Chain C: P.317 Chain D: F.31, T.32, Y.36, R.102 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain E: R.76, D.77, N.78, S.79 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain E: T.62, Y.64, T.73, I.74 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain E: R.91, A.92, E.93 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain B: L.131 Chain E: F.31, T.32, S.35, Y.36 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain F: T.32, F.33, N.81 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain G: S.57, R.59, F.67, S.68, G.69 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain G: P.162, V.163, K.164, A.165 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain H: S.57, R.59, S.68 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain H: P.64, R.66, Q.84 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain H: Q.116, N.178 Ligand excluded by PLIP

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

Arginase-2, mitochondrial: ABC
Fab C0020187 heavy chain (IgG1): DEF
Fab C0020187 light chain (IgG1): GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
HHH

E
III

F
JJJ

G
LLL

H
MMM

I
NNN

Arginase-2, mitochondrial

Fab C0020187 heavy chain (IgG1)

Fab C0020187 light chain (IgG1)

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