SMTL ID : 3iai.1 (1 other biounit)

Crystal structure of the catalytic domain of the tumor-associated human carbonic anhydrase IX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-MAN.1: 12 residues within 4Å: Chain A: R.33, P.34, Q.35, V.107, E.108, F.112, F.144, F.191, N.212, T.214, F.256 Ligands: TRS.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.35 Water bridges: A:V.107 NAG-NAG-BMA-MAN-MAN.2: 12 residues within 4Å: Chain B: R.33, P.34, Q.35, V.107, E.108, F.112, F.144, F.191, N.212, T.214, F.256 Ligands: TRS.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.35

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: H.92, H.94, E.104, H.117, T.198 Ligands: AZM.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:H.94, A:H.117 ZN.15: 6 residues within 4Å: Chain B: H.92, H.94, E.104, H.117, T.198 Ligands: AZM.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.92, B:H.94, B:H.117

2 x AZM: 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE(Non-covalent)

AZM.4: 13 residues within 4Å: Chain A: Q.90, H.92, H.94, E.104, H.117, V.119, V.128, L.197, T.198, T.199, W.208 Ligands: ZN.3, GOL.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.128 Hydrogen bonds: A:Q.90, A:T.198, A:T.198, A:T.199 Water bridges: A:T.199, A:T.199 AZM.16: 13 residues within 4Å: Chain B: Q.90, H.92, H.94, E.104, H.117, V.119, V.128, L.197, T.198, T.199, W.208 Ligands: ZN.15, GOL.17 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.128 Hydrogen bonds: B:Q.90, B:T.198, B:T.198, B:T.199

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: W.7, N.64, S.67, Q.69, Q.90, H.92, T.199 Ligands: AZM.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.64, A:Q.69, A:Q.90, A:T.199 Water bridges: A:Q.69, A:Q.69 GOL.6: 5 residues within 4Å: Chain A: Y.9, G.10, W.15, R.242 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.10 Water bridges: A:R.242, A:R.242 GOL.7: 4 residues within 4Å: Chain A: L.239, F.241, A.243 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.239 GOL.8: 8 residues within 4Å: Chain A: W.95, G.96, A.97, R.100, P.113, L.222, H.223, S.226 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.96, A:A.97, A:A.97, A:R.100, A:P.113, A:S.226 Water bridges: A:G.99 GOL.9: 7 residues within 4Å: Chain A: S.5, H.6, W.7, N.64, H.66, E.168, P.232 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.5, A:W.7, A:E.168 GOL.10: 4 residues within 4Å: Chain A: E.130, R.134 Chain B: E.130, R.134 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:E.130, B:R.134, B:R.134, A:R.134, A:R.134 Water bridges: B:R.127, A:A.126, A:E.130, A:E.130, A:E.130 GOL.11: 7 residues within 4Å: Chain A: R.25, F.26, N.248, G.249 Chain B: R.44, P.82 Ligands: PO4.24 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.44, A:R.25, A:R.25 GOL.17: 9 residues within 4Å: Chain B: N.64, H.66, S.67, Q.69, Q.90, H.92, H.94, T.199 Ligands: AZM.16 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.64, B:N.64, B:Q.69, B:Q.90 Water bridges: B:Q.69, B:H.94 GOL.18: 7 residues within 4Å: Chain B: R.8, Y.9, G.10, G.11, W.15, R.242 Ligands: GOL.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.10, B:G.11 Water bridges: B:R.8, B:R.242 GOL.19: 4 residues within 4Å: Chain B: L.239, F.241, A.243 Ligands: GOL.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.239 GOL.20: 8 residues within 4Å: Chain B: W.95, G.96, A.97, R.100, P.113, L.222, H.223, S.226 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.96, B:A.97, B:A.97, B:R.100, B:P.113, B:S.226 Water bridges: B:G.99, B:H.223 GOL.21: 3 residues within 4Å: Chain B: E.151, E.156, K.220 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.151, B:K.220, B:K.220 GOL.22: 6 residues within 4Å: Chain A: R.44 Chain B: R.25, F.26, N.248, G.249 Ligands: PO4.14 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.44, B:R.25, B:R.25

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.12: 4 residues within 4Å: Chain A: F.112, E.146, T.214 Ligands: NAG-NAG-BMA-MAN-MAN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.110, A:E.146 Water bridges: A:E.146 TRS.23: 3 residues within 4Å: Chain B: F.112, E.146 Ligands: NAG-NAG-BMA-MAN-MAN.2 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.214, B:T.214 Water bridges: B:H.110, B:H.110, B:E.146, B:E.146

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

PO4.13: 2 residues within 4Å: Chain A: G.1, R.17 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.4 Salt bridges: A:R.17 PO4.14: 3 residues within 4Å: Chain A: R.44, E.47 Ligands: GOL.22 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.44 PO4.24: 3 residues within 4Å: Chain B: R.44, E.47 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.47 Water bridges: B:R.44, B:E.47 Salt bridges: B:R.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alterio, V. et al., Crystal structure of the catalytic domain of the tumor-associated human carbonic anhydrase IX. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-09-08

Peptides

Carbonic anhydrase 9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carbonic anhydrase 9

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