SMTL ID : 6ss2.1

Structure of arginase-2 in complex with the inhibitory human antigen-binding fragment Fab C0021158

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-3-3-3-mer

Ligands

60 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: S.168, A.170, S.171, K.220, R.221, R.223 Ligand excluded by PLIP GOL.2: 7 residues within 4Å: Chain A: Q.304, T.305, G.308, G.309, H.310, I.311 Chain D: P.182 Ligand excluded by PLIP GOL.3: 3 residues within 4Å: Chain A: K.208, R.212 Ligands: GOL.11 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: T.251, R.253, E.254 Chain G: T.251, R.253 Ligands: GOL.43, GOL.82 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: R.36, Y.252, D.296, Q.304 Chain D: R.178, V.246, V.247 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: C.42, H.43, L.44 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: S.134, S.135, G.136 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: D.152, K.153, N.190, Y.191 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: T.237, L.238 Chain D: D.235, T.237 Ligands: GOL.48, GOL.87 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: T.132, T.133, S.134, N.137 Ligand excluded by PLIP GOL.11: 2 residues within 4Å: Chain A: K.208 Ligands: GOL.3 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain A: S.283, E.284, E.285 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: F.214, D.215, I.218, G.219, T.265 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain B: V.6, R.102, R.104 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain B: S.11, G.12, G.13, T.118 Ligands: SO4.29 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain B: V.174, H.175, T.176 Chain C: Q.175, S.176 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain C: T.9, Q.10, P.11, S.25 Ligand excluded by PLIP GOL.31: 7 residues within 4Å: Chain C: I.33, N.35, H.36, Y.37, N.56, K.71 Ligands: SO4.34 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain C: S.160, S.161, P.162 Ligand excluded by PLIP GOL.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.40: 6 residues within 4Å: Chain D: S.168, A.170, S.171, K.220, R.221, R.223 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain D: Q.304, T.305, G.308, G.309, H.310, I.311 Chain G: P.182 Ligand excluded by PLIP GOL.42: 3 residues within 4Å: Chain D: K.208, R.212 Ligands: GOL.50 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain A: T.251, R.253 Chain D: T.251, R.253, E.254 Ligands: GOL.4, GOL.82 Ligand excluded by PLIP GOL.44: 7 residues within 4Å: Chain D: R.36, Y.252, D.296, Q.304 Chain G: R.178, V.246, V.247 Ligand excluded by PLIP GOL.45: 3 residues within 4Å: Chain D: C.42, H.43, L.44 Ligand excluded by PLIP GOL.46: 3 residues within 4Å: Chain D: S.134, S.135, G.136 Ligand excluded by PLIP GOL.47: 4 residues within 4Å: Chain D: D.152, K.153, N.190, Y.191 Ligand excluded by PLIP GOL.48: 6 residues within 4Å: Chain D: T.237, L.238 Chain G: D.235, T.237 Ligands: GOL.9, GOL.87 Ligand excluded by PLIP GOL.49: 4 residues within 4Å: Chain D: T.132, T.133, S.134, N.137 Ligand excluded by PLIP GOL.50: 2 residues within 4Å: Chain D: K.208 Ligands: GOL.42 Ligand excluded by PLIP GOL.51: 3 residues within 4Å: Chain D: S.283, E.284, E.285 Ligand excluded by PLIP GOL.52: 5 residues within 4Å: Chain D: F.214, D.215, I.218, G.219, T.265 Ligand excluded by PLIP GOL.64: 3 residues within 4Å: Chain E: V.6, R.102, R.104 Ligand excluded by PLIP GOL.65: 5 residues within 4Å: Chain E: S.11, G.12, G.13, T.118 Ligands: SO4.68 Ligand excluded by PLIP GOL.66: 5 residues within 4Å: Chain E: V.174, H.175, T.176 Chain F: Q.175, S.176 Ligand excluded by PLIP GOL.69: 4 residues within 4Å: Chain F: T.9, Q.10, P.11, S.25 Ligand excluded by PLIP GOL.70: 7 residues within 4Å: Chain F: I.33, N.35, H.36, Y.37, N.56, K.71 Ligands: SO4.73 Ligand excluded by PLIP GOL.71: 3 residues within 4Å: Chain F: S.160, S.161, P.162 Ligand excluded by PLIP GOL.72: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.79: 6 residues within 4Å: Chain G: S.168, A.170, S.171, K.220, R.221, R.223 Ligand excluded by PLIP GOL.80: 7 residues within 4Å: Chain A: P.182 Chain G: Q.304, T.305, G.308, G.309, H.310, I.311 Ligand excluded by PLIP GOL.81: 3 residues within 4Å: Chain G: K.208, R.212 Ligands: GOL.89 Ligand excluded by PLIP GOL.82: 7 residues within 4Å: Chain D: T.251, R.253 Chain G: T.251, R.253, E.254 Ligands: GOL.4, GOL.43 Ligand excluded by PLIP GOL.83: 7 residues within 4Å: Chain A: R.178, V.246, V.247 Chain G: R.36, Y.252, D.296, Q.304 Ligand excluded by PLIP GOL.84: 3 residues within 4Å: Chain G: C.42, H.43, L.44 Ligand excluded by PLIP GOL.85: 3 residues within 4Å: Chain G: S.134, S.135, G.136 Ligand excluded by PLIP GOL.86: 4 residues within 4Å: Chain G: D.152, K.153, N.190, Y.191 Ligand excluded by PLIP GOL.87: 6 residues within 4Å: Chain A: D.235, T.237 Chain G: T.237, L.238 Ligands: GOL.9, GOL.48 Ligand excluded by PLIP GOL.88: 4 residues within 4Å: Chain G: T.132, T.133, S.134, N.137 Ligand excluded by PLIP GOL.89: 2 residues within 4Å: Chain G: K.208 Ligands: GOL.81 Ligand excluded by PLIP GOL.90: 3 residues within 4Å: Chain G: S.283, E.284, E.285 Ligand excluded by PLIP GOL.91: 5 residues within 4Å: Chain G: F.214, D.215, I.218, G.219, T.265 Ligand excluded by PLIP GOL.103: 3 residues within 4Å: Chain H: V.6, R.102, R.104 Ligand excluded by PLIP GOL.104: 5 residues within 4Å: Chain H: S.11, G.12, G.13, T.118 Ligands: SO4.107 Ligand excluded by PLIP GOL.105: 5 residues within 4Å: Chain H: V.174, H.175, T.176 Chain I: Q.175, S.176 Ligand excluded by PLIP GOL.108: 4 residues within 4Å: Chain I: T.9, Q.10, P.11, S.25 Ligand excluded by PLIP GOL.109: 7 residues within 4Å: Chain I: I.33, N.35, H.36, Y.37, N.56, K.71 Ligands: SO4.112 Ligand excluded by PLIP GOL.110: 3 residues within 4Å: Chain I: S.160, S.161, P.162 Ligand excluded by PLIP GOL.111: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

MN.14: 9 residues within 4Å: Chain A: H.99, W.120, D.122, H.124, D.126, D.230, E.275 Ligands: MN.15, SO4.22 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.99, A:D.122, A:D.126, A:D.230 MN.15: 7 residues within 4Å: Chain A: D.122, A.123, H.124, D.230, D.232 Ligands: MN.14, SO4.22 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.53: 9 residues within 4Å: Chain D: H.99, W.120, D.122, H.124, D.126, D.230, E.275 Ligands: MN.54, SO4.61 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.99, D:D.122, D:D.126, D:D.230 MN.54: 7 residues within 4Å: Chain D: D.122, A.123, H.124, D.230, D.232 Ligands: MN.53, SO4.61 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.122, D:H.124, D:D.230, D:D.232, D:D.232 MN.92: 9 residues within 4Å: Chain G: H.99, W.120, D.122, H.124, D.126, D.230, E.275 Ligands: MN.93, SO4.100 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.99, G:D.122, G:D.126, G:D.230 MN.93: 7 residues within 4Å: Chain G: D.122, A.123, H.124, D.230, D.232 Ligands: MN.92, SO4.100 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.122, G:H.124, G:D.230, G:D.232, G:D.232

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

SO4.16: 2 residues within 4Å: Chain A: R.199, R.203 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain A: P.56, N.67, P.68, R.69, P.158 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain A: K.17, R.18 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain A: L.157, P.158, G.159, F.160, S.161 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain A: R.221, Q.222 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain A: R.203, L.204, R.212 Ligand excluded by PLIP SO4.22: 11 residues within 4Å: Chain A: H.99, D.122, H.124, D.126, H.139, D.230, D.232, T.244, E.275 Ligands: MN.14, MN.15 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain A: L.44, K.45, D.46 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain A: H.185, K.189 Chain G: G.309 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain B: K.80 Chain F: P.64, R.66, Q.84 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: G.117, T.118, L.119 Ligands: GOL.26 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain C: K.71, S.72, G.73 Ligands: GOL.31 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain C: S.57, E.58, R.59 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain C: A.165, G.166 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain C: R.197, S.198 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain B: R.116 Chain C: T.47, A.48 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain C: S.29, S.30, T.74 Ligand excluded by PLIP SO4.55: 2 residues within 4Å: Chain D: R.199, R.203 Ligand excluded by PLIP SO4.56: 5 residues within 4Å: Chain D: P.56, N.67, P.68, R.69, P.158 Ligand excluded by PLIP SO4.57: 2 residues within 4Å: Chain D: K.17, R.18 Ligand excluded by PLIP SO4.58: 5 residues within 4Å: Chain D: L.157, P.158, G.159, F.160, S.161 Ligand excluded by PLIP SO4.59: 2 residues within 4Å: Chain D: R.221, Q.222 Ligand excluded by PLIP SO4.60: 3 residues within 4Å: Chain D: R.203, L.204, R.212 Ligand excluded by PLIP SO4.61: 11 residues within 4Å: Chain D: H.99, D.122, H.124, D.126, H.139, D.230, D.232, T.244, E.275 Ligands: MN.53, MN.54 Ligand excluded by PLIP SO4.62: 3 residues within 4Å: Chain D: L.44, K.45, D.46 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain A: G.309 Chain D: H.185, K.189 Ligand excluded by PLIP SO4.67: 4 residues within 4Å: Chain E: K.80 Chain I: P.64, R.66, Q.84 Ligand excluded by PLIP SO4.68: 4 residues within 4Å: Chain E: G.117, T.118, L.119 Ligands: GOL.65 Ligand excluded by PLIP SO4.73: 4 residues within 4Å: Chain F: K.71, S.72, G.73 Ligands: GOL.70 Ligand excluded by PLIP SO4.74: 3 residues within 4Å: Chain F: S.57, E.58, R.59 Ligand excluded by PLIP SO4.75: 2 residues within 4Å: Chain F: A.165, G.166 Ligand excluded by PLIP SO4.76: 2 residues within 4Å: Chain F: R.197, S.198 Ligand excluded by PLIP SO4.77: 3 residues within 4Å: Chain E: R.116 Chain F: T.47, A.48 Ligand excluded by PLIP SO4.78: 3 residues within 4Å: Chain F: S.29, S.30, T.74 Ligand excluded by PLIP SO4.94: 2 residues within 4Å: Chain G: R.199, R.203 Ligand excluded by PLIP SO4.95: 5 residues within 4Å: Chain G: P.56, N.67, P.68, R.69, P.158 Ligand excluded by PLIP SO4.96: 2 residues within 4Å: Chain G: K.17, R.18 Ligand excluded by PLIP SO4.97: 5 residues within 4Å: Chain G: L.157, P.158, G.159, F.160, S.161 Ligand excluded by PLIP SO4.98: 2 residues within 4Å: Chain G: R.221, Q.222 Ligand excluded by PLIP SO4.99: 3 residues within 4Å: Chain G: R.203, L.204, R.212 Ligand excluded by PLIP SO4.100: 11 residues within 4Å: Chain G: H.99, D.122, H.124, D.126, H.139, D.230, D.232, T.244, E.275 Ligands: MN.92, MN.93 Ligand excluded by PLIP SO4.101: 3 residues within 4Å: Chain G: L.44, K.45, D.46 Ligand excluded by PLIP SO4.102: 3 residues within 4Å: Chain D: G.309 Chain G: H.185, K.189 Ligand excluded by PLIP SO4.106: 4 residues within 4Å: Chain C: P.64, R.66, Q.84 Chain H: K.80 Ligand excluded by PLIP SO4.107: 4 residues within 4Å: Chain H: G.117, T.118, L.119 Ligands: GOL.104 Ligand excluded by PLIP SO4.112: 4 residues within 4Å: Chain I: K.71, S.72, G.73 Ligands: GOL.109 Ligand excluded by PLIP SO4.113: 3 residues within 4Å: Chain I: S.57, E.58, R.59 Ligand excluded by PLIP SO4.114: 2 residues within 4Å: Chain I: A.165, G.166 Ligand excluded by PLIP SO4.115: 2 residues within 4Å: Chain I: R.197, S.198 Ligand excluded by PLIP SO4.116: 3 residues within 4Å: Chain H: R.116 Chain I: T.47, A.48 Ligand excluded by PLIP SO4.117: 3 residues within 4Å: Chain I: S.29, S.30, T.74 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Austin, M. et al., Structural and functional characterization of C0021158, a high-affinity monoclonal antibody that inhibits Arginase 2 function via a novel non-competitive mechanism of action. Mabs

Release Date

2020-06-10

Peptides

Arginase-2, mitochondrial: ADG
Fab C0021158 heavy chain (IgG1): BEH
Fab C0021158 light chain (IgG1): CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

D
AAA

G
AAA

B
HHH

E
HHH

H
HHH

C
LLL

F
LLL

I
LLL

Arginase-2, mitochondrial

Fab C0021158 heavy chain (IgG1)

Fab C0021158 light chain (IgG1)

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