SMTL ID : 3n2c.2 (1 other biounit)

Crystal structure of prolidase eah89906 complexed with n-methylphosphonate-l-proline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-octamer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.65, H.67, K.190, D.323 Ligands: ZN.2, LWY.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.65, A:H.67, A:D.323 ZN.2: 5 residues within 4Å: Chain A: K.190, H.231, H.251 Ligands: ZN.1, LWY.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.231, A:H.251 ZN.4: 7 residues within 4Å: Chain B: H.65, H.67, A.108, K.190, D.323 Ligands: ZN.5, LWY.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.65, B:H.67, B:D.323 ZN.5: 5 residues within 4Å: Chain B: K.190, H.231, H.251 Ligands: ZN.4, LWY.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.231, B:H.251 ZN.7: 6 residues within 4Å: Chain C: H.65, H.67, A.108, K.190, D.323 Ligands: LWY.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.65, C:H.67, C:D.323 ZN.8: 5 residues within 4Å: Chain C: H.142, K.190, H.231, H.251 Ligands: LWY.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.231, C:H.251 ZN.10: 6 residues within 4Å: Chain D: H.65, H.67, A.108, K.190, D.323 Ligands: LWY.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.65, D:H.67, D:D.323 ZN.11: 5 residues within 4Å: Chain D: H.142, K.190, H.231, H.251 Ligands: LWY.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.231, D:H.251 ZN.13: 6 residues within 4Å: Chain E: H.65, H.67, A.108, K.190, D.323 Ligands: LWY.15 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.65, E:H.67, E:D.323 ZN.14: 5 residues within 4Å: Chain E: H.142, K.190, H.231, H.251 Ligands: LWY.15 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.231, E:H.251 ZN.16: 7 residues within 4Å: Chain F: H.65, H.67, A.108, K.190, D.323 Ligands: ZN.17, LWY.18 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.65, F:H.67, F:D.323 ZN.17: 5 residues within 4Å: Chain F: K.190, H.231, H.251 Ligands: ZN.16, LWY.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.231, F:H.251 ZN.19: 7 residues within 4Å: Chain G: H.65, H.67, A.108, K.190, D.323 Ligands: ZN.20, LWY.21 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.65, G:H.67, G:D.323 ZN.20: 5 residues within 4Å: Chain G: K.190, H.231, H.251 Ligands: ZN.19, LWY.21 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.231, G:H.251 ZN.22: 7 residues within 4Å: Chain H: H.65, H.67, A.108, K.190, D.323 Ligands: ZN.23, LWY.24 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:H.65, H:H.67, H:D.323 ZN.23: 5 residues within 4Å: Chain H: K.190, H.231, H.251 Ligands: ZN.22, LWY.24 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:H.231, H:H.251

8 x LWY: 1-[(R)-hydroxy(methyl)phosphoryl]-L-proline(Non-covalent)

LWY.3: 15 residues within 4Å: Chain A: H.65, H.67, L.75, H.142, K.190, V.197, A.198, H.231, Y.233, H.251, T.276, D.323, L.325 Ligands: ZN.1, ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.276 Hydrogen bonds: A:V.197, A:A.198, A:Y.233 Salt bridges: A:H.142, A:H.231, A:H.251, A:D.323 LWY.6: 16 residues within 4Å: Chain B: H.65, H.67, H.142, K.190, G.196, V.197, A.198, H.231, Y.233, H.251, Y.277, L.280, D.323, L.325 Ligands: ZN.4, ZN.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.277, B:L.280 Hydrogen bonds: B:V.197, B:A.198, B:Y.233 Salt bridges: B:H.142, B:H.231, B:H.251, B:D.323 LWY.9: 16 residues within 4Å: Chain C: H.65, H.67, L.75, H.142, K.190, G.196, V.197, A.198, H.231, Y.233, H.251, Y.277, D.323, L.325 Ligands: ZN.7, ZN.8 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.277 Hydrogen bonds: C:V.197, C:A.198, C:Y.233 Salt bridges: C:H.142, C:H.231, C:H.251, C:D.323 LWY.12: 17 residues within 4Å: Chain D: H.65, H.67, L.75, H.142, K.190, G.196, V.197, A.198, H.231, Y.233, H.251, T.276, Y.277, D.323, L.325 Ligands: ZN.10, ZN.11 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:T.276, D:Y.277 Hydrogen bonds: D:V.197, D:A.198, D:Y.233, D:Y.233 Salt bridges: D:H.142, D:H.231, D:D.323 LWY.15: 15 residues within 4Å: Chain E: H.65, H.67, L.75, H.142, K.190, G.196, V.197, A.198, H.231, Y.233, H.251, D.323, L.325 Ligands: ZN.13, ZN.14 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:V.197, E:A.198, E:Y.233, E:Y.233 Salt bridges: E:H.142, E:H.231, E:H.251, E:D.323 LWY.18: 15 residues within 4Å: Chain F: H.65, H.67, H.142, K.190, G.196, V.197, A.198, H.231, Y.233, H.251, Y.277, D.323, L.325 Ligands: ZN.16, ZN.17 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:Y.277 Hydrogen bonds: F:V.197, F:A.198, F:Y.233, F:Y.233 Salt bridges: F:H.142, F:H.231, F:D.323 LWY.21: 15 residues within 4Å: Chain G: H.65, H.67, L.75, H.142, K.190, V.197, A.198, H.231, Y.233, H.251, T.276, D.323, L.325 Ligands: ZN.19, ZN.20 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:T.276 Hydrogen bonds: G:V.197, G:A.198, G:Y.233 Salt bridges: G:H.142, G:H.231, G:H.251, G:D.323 LWY.24: 15 residues within 4Å: Chain H: H.65, H.67, L.75, H.142, K.190, G.196, V.197, A.198, H.231, Y.233, H.251, D.323, L.325 Ligands: ZN.22, ZN.23 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:V.197, H:A.198, H:Y.233, H:Y.233 Salt bridges: H:H.142, H:H.231, H:H.251, H:D.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, D.F. et al., Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily . Biochemistry (2010)

Release Date

2010-06-02

Peptides

PROLIDASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

E
M

F
N

G
O

H
P

PROLIDASE

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